{ "checkpoint": "CIDM_iReview_P0_DeepReview_Closure_173_v1.1", "as_of": "2026-10-03", "scope": "POST_BASE_DELTA_P0", "publication_denominator": 1947, "p0_reviewed": 173, "p0_coverage": 1.0, "review_depth_counts": { "ABSTRACT_REVIEWED": 125, "METADATA_REVIEWED": 8, "FULL_TEXT_REVIEWED": 40 }, "human_gate": "OPEN", "formal_accept": 0, "boundary": "AI prereview/evidence review at the source depth actually inspected; not external peer review or Human Gate acceptance.", "records": [ { "review_event_id": "IRD-20261003-B01-01", "object_id": "CIDM-WORK-1775", "pmid": "37932121", "year": 2023, "title": "Therapeutic Phage Monitoring: A Review", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Review", "research_question": "What monitoring framework should accompany therapeutic phage therapy to measure in-vivo efficacy, host responses, ecological effects and support dose optimisation?", "methods_summary": "Narrative/conceptual review of therapeutic phage monitoring across phage concentrations, immune responses, ecological changes, diagnostic surrogates and quality indicators.", "main_finding": "Therapeutic phage monitoring is proposed as a core component of phage-therapy protocols; longitudinal measurement of phage exposure, immune responses and ecological effects could support precision dosing, efficacy surrogates and product quality assurance.", "limitations": "A review/proposal rather than a prospective validation study; monitoring standards, clinically validated thresholds and evidence that TPM improves outcomes remain underdeveloped.", "cidm_contribution": "Direct CIDM/WIMR authorship; contributes a framework for phage-therapy implementation, monitoring and translational infectious-diseases practice.", "contradictions_unknowns": "Which TPM measures best predict clinical success, how often to sample, and how to standardise assays across phage products and centres remain open.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37932121/" }, { "review_event_id": "IRD-20261003-B01-02", "object_id": "CIDM-WORK-1776", "pmid": "30853132", "year": 2019, "title": "Genetic differences in Chlamydia pecorum between neighbouring sub-populations of koalas (Phascolarctos cinereus)", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Observational molecular epidemiology", "research_question": "Do neighbouring koala sub-populations with different chlamydiosis expression carry different Chlamydia pecorum sequence types?", "methods_summary": "MLST using seven housekeeping loci on C. pecorum samples from two Liverpool Plains koala sub-populations sampled in 2015–2017.", "main_finding": "Sequence-type frequencies differed between sub-populations and ST69 was associated with clinical disease, but the same ST has also been observed in subclinical infection; strain emergence and/or limited resolution of the MLST scheme may explain the pattern.", "limitations": "Local two-population design; housekeeping-locus MLST may not capture virulence determinants or fine-scale transmission; association does not establish pathogenic causality.", "cidm_contribution": "Direct Molecular Mycology/CIDM participation; links pathogen genotyping with wildlife disease epidemiology and demonstrates limits of typing resolution.", "contradictions_unknowns": "Whole-genome or virulence-marker data are needed to determine whether ST69 itself is pathogenic or simply marks recent introduction.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30853132/" }, { "review_event_id": "IRD-20261003-B01-03", "object_id": "CIDM-WORK-1777", "pmid": "12475633", "year": 2002, "title": "Metabolites released by Cryptococcus neoformans var. neoformans and var. gattii differentially affect human neutrophil function", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Experimental translational microbiology", "research_question": "Do extracellular metabolites released by C. neoformans var. neoformans and var. gattii differentially modulate neutrophil viability and function?", "methods_summary": "Rat infection observations, magnetic-resonance spectroscopy of heat-inactivated fungal supernatants, and human-neutrophil functional assays at physiologic and acidic pH.", "main_finding": "The two varieties released broadly similar but quantitatively distinct metabolites; var. gattii supernatant contained acetoin and dihydroxyacetone and produced distinct effects on neutrophil oxidative burst, viability and migration, supporting metabolite-mediated host–pathogen modulation.", "limitations": "One strain of each variety; largely in-vitro/ex-vivo functional assays; metabolite concentrations and relevance in human lesions are uncertain.", "cidm_contribution": "Classic CIDM cryptococcosis work integrating mycology, spectroscopy and innate immunity.", "contradictions_unknowns": "Which metabolites dominate in-vivo immune modulation and whether these differences explain clinical tropism require validation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/12475633/" }, { "review_event_id": "IRD-20261003-B01-04", "object_id": "CIDM-WORK-1778", "pmid": "25409355", "year": 2014, "title": "Hospital-onset Gram-negative Surveillance Program annual report, 2011", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "National antimicrobial-resistance surveillance", "research_question": "What was the prevalence of key antimicrobial resistance phenotypes among hospital-onset E. coli, Klebsiella and Enterobacter isolates in the 2011 Australian surveillance program?", "methods_summary": "Period-prevalence surveillance across Australian diagnostic laboratories; 1,827 E. coli, 537 Klebsiella spp. and 269 Enterobacter spp. tested using Vitek 2 and CLSI 2012 breakpoints.", "main_finding": "Third-generation cephalosporin, fluoroquinolone and gentamicin non-susceptibility were present at clinically relevant levels, and eight isolates carried IMP-4 carbapenemase, documenting emerging hospital Gram-negative resistance.", "limitations": "Sentinel/period-prevalence design; laboratory isolates may not represent all hospitals or patient-level outcomes; historical 2011 resistance landscape and breakpoint definitions.", "cidm_contribution": "CIDM contribution via David Mitchell and national AGAR surveillance; directly relevant to antimicrobial-resistance intelligence.", "contradictions_unknowns": "Longitudinal comparability depends on participating sites, sampling frame, breakpoints and subsequent resistance evolution.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/25409355/" }, { "review_event_id": "IRD-20261003-B01-05", "object_id": "CIDM-WORK-1779", "pmid": "24859394", "year": 2014, "title": "Hepatitis C virus infection mediates cholesteryl ester synthesis to facilitate infectious particle production", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic virology", "research_question": "Does HCV-induced cholesterol accumulation drive cholesteryl ester synthesis that is required for production of infectious lipoviral particles?", "methods_summary": "HCV cell-culture experiments, ACAT gene-expression analysis, human liver-biopsy comparison, pharmacological ACAT inhibition and density-gradient analysis of viral particles.", "main_finding": "HCV infection increased ACAT expression and cholesteryl ester synthesis; ACAT inhibition reduced infectious-virus production without blocking RNA replication and increased particle density, implicating host cholesterol esterification in virion lipidation.", "limitations": "Predominantly in-vitro pharmacology; inhibitor specificity and clinical feasibility require validation; biopsy associations do not prove causality.", "cidm_contribution": "CIDM-linked HCV host-factor research connecting viral assembly to host lipid metabolism.", "contradictions_unknowns": "Whether ACAT targeting is safe and effective in-vivo and whether effects generalise across HCV genotypes remain unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24859394/" }, { "review_event_id": "IRD-20261003-B01-06", "object_id": "CIDM-WORK-1780", "pmid": "24998883", "year": 2015, "title": "Instrumental support to facilitate hepatitis C treatment adherence: working around shortfalls in shared-care", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Qualitative health-services research", "research_question": "How do physicians and nurses support HCV treatment adherence when multidisciplinary shared-care is incomplete or unavailable?", "methods_summary": "2012 interview study using a purposive sample of 20 Australian physicians and nurses.", "main_finding": "Clinicians filled shared-care gaps through advocacy, pragmatic problem-solving, engagement and emotional support; these strategies may help adherence but can push clinicians beyond their disciplinary expertise.", "limitations": "Small purposive sample, self-report and qualitative inference; conducted in the interferon-treatment era, limiting direct applicability to modern DAA care.", "cidm_contribution": "CIDM-associated clinical HCV work addressing implementation and care-delivery barriers rather than only virology.", "contradictions_unknowns": "Effectiveness, cost and safety of clinician-provided instrumental support need prospective evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24998883/" }, { "review_event_id": "IRD-20261003-B01-07", "object_id": "CIDM-WORK-1781", "pmid": "25041771", "year": 2014, "title": "Vancomycin-associated drug reaction with eosinophilia and systemic symptoms syndrome", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Case series / clinical review", "research_question": "Can vancomycin trigger definite DRESS syndrome and what clinical recognition issues does this raise?", "methods_summary": "Report of three definite vancomycin-associated DRESS cases with literature review.", "main_finding": "The paper documents vancomycin as a cause of delayed, potentially life-threatening multisystem DRESS and highlights the need for recognition of fever, rash, eosinophilia and organ involvement.", "limitations": "Three-case series; no incidence estimate or comparator; causality rests on clinical attribution and case definitions.", "cidm_contribution": "Clinically relevant CIDM-linked adverse-drug-reaction signal at the infection–immunology interface.", "contradictions_unknowns": "Risk factors, genetic susceptibility and optimal monitoring for vancomycin-associated DRESS remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/25041771/" }, { "review_event_id": "IRD-20261003-B01-08", "object_id": "CIDM-WORK-1782", "pmid": "25246395", "year": 2014, "title": "Cross-genotypic examination of hepatitis C virus polymerase inhibitors reveals a novel mechanism of action for thumb binders", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic antiviral pharmacology", "research_question": "How broadly do HCV non-nucleoside polymerase inhibitors act across genotypes 1, 2 and 3, and do different binding classes alter polymerase function differently?", "methods_summary": "Six NNIs tested against G1b, G2a and G3a replicons plus recombinant G1b/G3a RNA-dependent RNA polymerases.", "main_finding": "Only nesbuvir showed broad G1–G3 activity; JTK-109 had reduced G2 activity; several NNIs lost potency in non-G1 viruses. Thumb-II binders inhibited primer-dependent but paradoxically enhanced de-novo polymerase activity at higher concentrations.", "limitations": "Replicon/recombinant-enzyme systems; no clinical outcomes; in-vitro concentrations and resistance determinants may not translate directly to patients.", "cidm_contribution": "CIDM-associated mechanistic HCV antiviral work clarifying genotype coverage and polymerase-inhibitor biology.", "contradictions_unknowns": "Clinical relevance of the de-novo activity enhancement and its interaction with combination therapy require further study.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/25246395/" }, { "review_event_id": "IRD-20261003-B01-09", "object_id": "CIDM-WORK-1783", "pmid": "24335707", "year": 2014, "title": "Hepatic metallothionein expression in chronic hepatitis C virus infection is IFNL3 genotype-dependent", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human molecular association study", "research_question": "Does IFNL3 genotype define a distinctive interferon-stimulated-gene pattern that may help explain HCV clearance?", "methods_summary": "Gene-expression analysis of HCV-infected liver biopsies and peripheral blood stratified by IFNL3 rs8099917 genotype, with attention to metallothioneins and fibrosis.", "main_finding": "Responder genotype was associated with higher hepatic metallothionein expression, lower fibrosis scores and overall lower hepatic ISGs; peripheral blood showed a contrasting ISG pattern. Metallothioneins were proposed as a biologically relevant component of the IFNL3 effect.", "limitations": "Association-based human expression study; causality and therapeutic value of metallothionein induction were not established; interferon-era context.", "cidm_contribution": "CIDM-linked translational HCV immunogenetics connecting host genotype, hepatic gene expression and fibrosis.", "contradictions_unknowns": "Whether metallothioneins are causal mediators of clearance and useful therapeutic targets remains to be tested.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24335707/" }, { "review_event_id": "IRD-20261003-B01-10", "object_id": "CIDM-WORK-1784", "pmid": "24768758", "year": 2014, "title": "IFNL3 polymorphisms predict response to therapy in chronic hepatitis C genotype 2/3 infection", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Large treatment-response cohort", "research_question": "Do IFNL3 polymorphisms predict sustained virological response in HCV genotype 2/3 infection?", "methods_summary": "Cohort of 1,002 Caucasian HCV-2/3 patients treated with pegylated interferon-alpha/ribavirin and genotyped for rs12979860 and rs8099917.", "main_finding": "Responder genotypes strongly predicted SVR and added information particularly when rapid virological response was absent; IFNL3 genotyping was proposed to support treatment decisions.", "limitations": "Caucasian interferon-era cohort; treatment landscape has since changed substantially with DAAs; observational treatment-response analysis.", "cidm_contribution": "CIDM-linked international HCV pharmacogenetics and treatment-response research.", "contradictions_unknowns": "Modern clinical utility is limited in DAA-era care, but biological relevance to host antiviral response remains.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24768758/" }, { "review_event_id": "IRD-20261003-B01-11", "object_id": "CIDM-WORK-1785", "pmid": "24861641", "year": 2014, "title": "A summary of the 20th International Symposium on Hepatitis C Virus and Related Viruses", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Conference synthesis / review", "research_question": "What were the major scientific advances presented at the 20th International Symposium on HCV and Related Viruses?", "methods_summary": "Narrative synthesis of meeting highlights from an international HCV symposium held in Melbourne in October 2013.", "main_finding": "The article summarises contemporaneous advances in HCV molecular biology, host response and therapeutics rather than presenting a single new experiment.", "limitations": "Selective meeting summary, not systematic review or primary research; content reflects a 2013 scientific snapshot.", "cidm_contribution": "Shows CIDM participation in broader HCV scientific synthesis and network knowledge exchange.", "contradictions_unknowns": "Individual claims require return to the original conference studies/publications for evidentiary assessment.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24861641/" }, { "review_event_id": "IRD-20261003-B01-12", "object_id": "CIDM-WORK-1786", "pmid": "24123215", "year": 2014, "title": "A new role for IKK-alpha in hepatitis C virus-induced lipogenesis", "access_level": "METADATA+COMMENTARY_SUMMARY", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Commentary", "research_question": "How should a newly described IKK-alpha–dependent lipogenic pathway in HCV assembly be interpreted biologically?", "methods_summary": "Commentary on prior primary research; PubMed identifies the item as CommentOn a 2013 Nature Medicine article. No independent experimental dataset is indexed for this paper.", "main_finding": "The commentary highlights a proposed NF-kB-independent nuclear role for IKK-alpha in HCV-induced lipogenesis and viral assembly.", "limitations": "Not primary research; mechanistic claims originate from the commented-on study and should not be attributed as newly demonstrated by this paper itself.", "cidm_contribution": "CIDM-linked scientific interpretation of host-factor mechanisms in HCV assembly.", "contradictions_unknowns": "Evidence strength should be assessed from the primary Nature Medicine study rather than this commentary alone.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24123215/" }, { "review_event_id": "IRD-20261003-B01-13", "object_id": "CIDM-WORK-1787", "pmid": "23998260", "year": 2014, "title": "Hepatic lesions and eosinophilia in an urban dweller", "access_level": "METADATA_CASE_SUMMARY", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Case report / image", "research_question": "What diagnosis should be considered in an urban patient with hepatic lesions and eosinophilia?", "methods_summary": "Indexed case report/image; no attributable abstract was recovered in this pass. PubMed indexing identifies Fasciola hepatica/fascioliasis, imaging, eosinophilia and triclabendazole treatment.", "main_finding": "The indexed record supports a clinical teaching case of fascioliasis presenting with hepatic lesions and eosinophilia.", "limitations": "No abstract/full text inspected in this pass; details beyond indexed terms must remain provisional.", "cidm_contribution": "CIDM-linked clinical infectious-disease diagnostic teaching case.", "contradictions_unknowns": "Clinical presentation, diagnostic sequence and treatment response should be verified from full text before deep-review completion.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/23998260/" }, { "review_event_id": "IRD-20261003-B01-14", "object_id": "CIDM-WORK-1788", "pmid": "24045339", "year": 2014, "title": "IFNL3 mediates interaction between innate immune cells: Implications for hepatitis C virus pathogenesis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human immunology / functional expression study", "research_question": "How are IFNL3 and its receptor expressed across innate immune-cell subsets and HCV-infected liver, and how do these cells respond to IFNL3?", "methods_summary": "Expression analysis of IFNL3/IFNLR1 in blood immune subsets and HCV liver tissue, functional response assays, and IFNL3 SNP genotyping.", "main_finding": "Blood innate immune cells expressed substantial IFNL3-related signals; pDCs were prominent in the IFNL3/IFNLR1 axis and PBMCs, monocytes and pDCs responded to IFNL3. No genotype-dependent expression difference was detected for the studied SNPs.", "limitations": "Expression/response study does not fully resolve the causal mechanism by which IFNL3 genotype alters HCV clearance; tissue and cell-subset complexity remains.", "cidm_contribution": "CIDM-linked work connecting HCV immunogenetics with innate-cell functional biology.", "contradictions_unknowns": "How genetic variants alter downstream cell behaviour without clear expression differences remains a mechanistic gap.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24045339/" }, { "review_event_id": "IRD-20261003-B01-15", "object_id": "CIDM-WORK-1789", "pmid": "24912485", "year": 2015, "title": "A randomized study of standard versus double dose oseltamivir for treating influenza in the community", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Randomized controlled trial", "research_question": "Does double-dose oseltamivir improve clinical/virological outcomes or reduce emergence of resistance compared with standard dose in community influenza?", "methods_summary": "Unblinded randomised trial; 52 confirmed influenza patients received 5 days of standard- or double-dose oseltamivir.", "main_finding": "Double dosing did not improve clinical resolution or viral clearance and did not prevent oseltamivir resistance; gastrointestinal adverse events were more frequent with double dose.", "limitations": "Small, underpowered, unblinded trial; only 52 participants and few resistant strains.", "cidm_contribution": "CIDM-linked clinical influenza and antiviral-resistance trial through Dominic Dwyer.", "contradictions_unknowns": "Larger studies would be needed to assess rare resistance outcomes or specific high-risk subgroups.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24912485/" }, { "review_event_id": "IRD-20261003-B01-16", "object_id": "CIDM-WORK-1790", "pmid": "25053565", "year": 2014, "title": "Endocannabinoid CB1 antagonists inhibit hepatitis C virus production, providing a novel class of antiviral host-targeting agents", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic antiviral host-target study", "research_question": "Can blockade of host cannabinoid receptor CB1 suppress HCV replication/production by altering lipid metabolism?", "methods_summary": "JFH1 cell-culture and subgenomic-replicon models, pharmacological CB1 antagonist AM251, lipid-gene expression assays and CB1 shRNA knockdown.", "main_finding": "CB1 blockade reduced HCV RNA, protein, particle production and infectivity, shifted lipid metabolism away from lipogenesis and was supported by CB1 knockdown, suggesting a host-target antiviral mechanism.", "limitations": "In-vitro proof-of-concept; AM251 and CB1 blockade have translational/safety constraints; no in-vivo efficacy shown.", "cidm_contribution": "CIDM-linked host-targeting antiviral work extending HCV biology into lipid/endocannabinoid pathways.", "contradictions_unknowns": "Whether a clinically tolerable CB1-targeting strategy can retain antiviral effect in vivo remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/25053565/" }, { "review_event_id": "IRD-20261003-B01-17", "object_id": "CIDM-WORK-1791", "pmid": "30036666", "year": 2019, "title": "The epidemiology and clinical manifestations of mucormycosis: a systematic review and meta-analysis of case reports", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Systematic review / pooled case analysis", "research_question": "What are the contemporary epidemiology, manifestations, predisposing factors and causative Mucorales species in adult mucormycosis?", "methods_summary": "MEDLINE/EMBASE search (2000–Jan 2017); 600 reports comprising 851 adult proven/probable cases; descriptive and multivariable analyses.", "main_finding": "Diabetes was the most common underlying condition; different host factors were associated with distinct clinical forms; Rhizopus was most common, and overall reported mortality was 46%.", "limitations": "Case-report/series evidence is highly susceptible to publication and selection bias; species identified in only about half of cases; adult-only retrospective literature.", "cidm_contribution": "Direct CIDMLS/Sharon Chen contribution to international invasive-fungal-disease epidemiology.", "contradictions_unknowns": "Population incidence, diagnostic-era trends and treatment-effect estimates require prospective registry or cohort data.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30036666/" }, { "review_event_id": "IRD-20261003-B01-18", "object_id": "CIDM-WORK-1792", "pmid": "30509777", "year": 2019, "title": "Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Systematic review + global survey", "research_question": "How did the global and regional distribution of HIV-1 subtypes and recombinants change from 1990 to 2015?", "methods_summary": "Systematic review plus global expert survey; 2,203 datasets, 383,519 samples from 116 countries; country estimates weighted by UNAIDS PLHIV estimates across four periods.", "main_finding": "Subtype C remained dominant globally, while recombinants increased and represented about 22.8% of infections in 2010–15; HIV molecular diversity is regionally heterogeneous and evolving.", "limitations": "Heterogeneous sampling, publication delay/bias, incomplete national coverage and weighting assumptions; sequence datasets are not probability samples of populations.", "cidm_contribution": "CIDM/Dwyer-linked global molecular epidemiology with direct relevance to diagnostics, surveillance and vaccine design.", "contradictions_unknowns": "More representative and continuously updated sequencing surveillance is needed, especially for under-sampled regions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30509777/" }, { "review_event_id": "IRD-20261003-B01-19", "object_id": "CIDM-WORK-1793", "pmid": "30723271", "year": 2019, "title": "A variant in the MICA gene is associated with liver fibrosis progression in chronic hepatitis C through TGF-β1 dependent mechanisms", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human genetics + mechanistic study", "research_question": "Are MICA/DEPDC5 risk variants associated with HCV fibrosis progression, and what biological mechanism could explain the association?", "methods_summary": "Genetic/phenotypic analysis in 1,689 chronic-HCV/HCV-HCC patients, expression analyses in liver/serum and hepatic-stellate-cell experiments involving TGF-beta1.", "main_finding": "The MICA T allele was associated with greater fibrosis stage/progression and lower MICA expression; TGF-beta1 suppressed MICA in stellate cells, suggesting a pathway linking genotype to fibrosis biology.", "limitations": "Genetic association does not by itself prove causation; mechanistic support is partly experimental/in-vitro; the variant was not associated with HCC susceptibility in this cohort.", "cidm_contribution": "CIDM-linked international liver-disease genetics integrating clinical cohorts with mechanistic fibrosis biology.", "contradictions_unknowns": "Whether MICA is a therapeutically actionable mediator and whether effects generalise across ancestries require validation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30723271/" }, { "review_event_id": "IRD-20261003-B01-20", "object_id": "CIDM-WORK-1794", "pmid": "30905683", "year": 2019, "title": "KLRG1+ natural killer cells exert a novel antifibrotic function in chronic hepatitis B", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human immunology + ex-vivo functional study", "research_question": "What role do KLRG1-positive NK cells play in chronic hepatitis B and liver fibrosis?", "methods_summary": "Blood/liver NK-cell phenotyping in healthy individuals and CHB patients, flow cytometry, in-vitro stimulation, hepatic-stellate-cell cytotoxicity/apoptosis assays.", "main_finding": "KLRG1+ NK cells were expanded in CHB, showed strong cytotoxic/IFN-gamma responses against stellate cells and induced TRAIL-dependent HSC apoptosis; higher frequency was associated with lower fibrosis stage.", "limitations": "Cross-sectional human associations and ex-vivo functional assays; no interventional evidence that manipulating KLRG1+ NK cells changes fibrosis clinically.", "cidm_contribution": "CIDM-linked translational hepatitis immunology identifying a potential antifibrotic immune-cell phenotype.", "contradictions_unknowns": "Causal role in vivo, therapeutic manipulability and longitudinal relationship with fibrosis progression remain unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30905683/" }, { "review_event_id": "IRD-20261003-B02-01", "object_id": "CIDM-WORK-1795", "pmid": "30601153", "year": 2019, "title": "Associations between baseline biomarkers and lung function in HIV-positive individuals", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Longitudinal cohort biomarker analysis", "research_question": "Are baseline inflammatory/coagulation biomarkers associated with baseline lung function and subsequent lung-function decline in HIV-positive adults?", "methods_summary": "START pulmonary substudy; 903 participants with baseline biomarkers and spirometry, with longitudinal follow-up among those with repeat spirometry. Multivariable regression related biomarkers to FEV1, FVC, FEV1/FVC and longitudinal slopes.", "main_finding": "Higher systemic inflammatory markers, including hsCRP and IL-6, were associated with worse baseline lung function; D-dimer and IL-6 were associated with greater airflow obstruction. Baseline biomarkers did not predict subsequent lung-function decline over median 3.9 years.", "limitations": "Observational biomarker associations; early HIV cohort with high baseline CD4 counts may limit generalisability; baseline biomarkers may not capture time-varying inflammatory burden.", "cidm_contribution": "Included through verified CIDM roster/core-person lineage; contributes to HIV systemic-inflammation and respiratory-outcome evidence.", "contradictions_unknowns": "Why cross-sectional inflammatory associations do not translate to longitudinal decline remains uncertain; other time-varying or pulmonary-specific biomarkers may be more informative.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30601153/" }, { "review_event_id": "IRD-20261003-B02-02", "object_id": "CIDM-WORK-1796", "pmid": "31312748", "year": 2019, "title": "Comparison of an ordinal endpoint to time-to-event, longitudinal, and binary endpoints for use in evaluating treatments for severe influenza requiring hospitalization", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Methodological endpoint-comparison study", "research_question": "How does a six-category day-7 ordinal clinical-status endpoint compare with time-to-event, longitudinal and binary endpoints for trials of severe influenza requiring hospitalisation?", "methods_summary": "Statistical comparison of candidate endpoints using the FLU-IVIG severe-influenza trial framework, examining power and behaviour of an ordinal proportional-odds endpoint against alternative endpoint types under varying assumptions.", "main_finding": "The ordinal endpoint was presented as an efficient way to use the full range of patient clinical status and can provide competitive or superior statistical power under plausible trial scenarios compared with simpler binary or time-to-event endpoints.", "limitations": "Methodological conclusions depend on assumed outcome distributions, treatment effects and model assumptions; proportional-odds violations and clinical interpretability remain important considerations.", "cidm_contribution": "Included through institutional-roster GREEN-A lineage; relevant to design and analysis of hospitalised severe-influenza treatment trials.", "contradictions_unknowns": "No single endpoint is universally optimal; performance depends on disease trajectory, timing and whether proportional-odds assumptions are reasonable.", "confidence": "MEDIUM", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6609815/" }, { "review_event_id": "IRD-20261003-B02-03", "object_id": "CIDM-WORK-1797", "pmid": "30958539", "year": 2019, "title": "Hepatitis C Virus Genotype 8 Infection-Successful Treatment With Sofosbuvir/Velpatasvir", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Case report / letter", "research_question": "Can HCV genotype 8 infection be successfully treated with sofosbuvir/velpatasvir?", "methods_summary": "Case-based report/letter describing genotype-8 HCV infection and treatment outcome.", "main_finding": "The publication reports successful treatment of HCV genotype 8 with sofosbuvir/velpatasvir.", "limitations": "PubMed record has no abstract; single-case evidence cannot establish population efficacy or comparative effectiveness.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; adds rare-genotype HCV treatment experience.", "contradictions_unknowns": "General effectiveness across genotype-8 infections and diverse patient populations requires larger clinical evidence.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30958539/" }, { "review_event_id": "IRD-20261003-B02-04", "object_id": "CIDM-WORK-1798", "pmid": "30606127", "year": 2019, "title": "Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC APTIMA assays for detection of Neisseria gonorrhoeae and Chlamydia trachomatis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic accuracy comparison", "research_question": "How does an in-house duplex real-time PCR perform against commercial APTIMA assays for detecting N. gonorrhoeae and C. trachomatis in urine and extragenital specimens?", "methods_summary": "Urine, oropharyngeal and anorectal specimens from 200 MSM were tested; in-house duplex PCR was compared with APTIMA reference assays.", "main_finding": "The in-house PCR showed very high agreement with APTIMA. Chlamydia performance was 100% for sensitivity/specificity in the reported dataset, while gonorrhoea sensitivity was lower by specimen type but specificity and PPV were 100%.", "limitations": "Single study population; APTIMA was used as comparator rather than an independent composite reference standard; extragenital performance needs broader validation.", "cidm_contribution": "Verified CIDM-person lineage through David A Lewis; supports practical STI diagnostic assay evaluation.", "contradictions_unknowns": "Lower gonorrhoea sensitivity relative to excellent specificity raises the question of false negatives in real-world screening.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30606127/" }, { "review_event_id": "IRD-20261003-B02-05", "object_id": "CIDM-WORK-1799", "pmid": "31551015", "year": 2019, "title": "Identification of the environmental source of infection for a domestic ferret with cryptococcosis", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Veterinary case investigation / molecular epidemiology", "research_question": "Could the environmental source of cryptococcosis in a domestic ferret be identified and linked molecularly to the clinical isolate?", "methods_summary": "Clinical case investigation with environmental sampling, ferret nasal swabs, culture, species/molecular typing and MLST; full text and supplement were available.", "main_finding": "A hollow eucalypt log was heavily contaminated with C. gattii VGI and C. neoformans VNI. MLST linked C. gattii VGI from the log to disease isolates, strongly supporting the log as the point source.", "limitations": "Single household/case setting; not all environmental exposure routes can be excluded; WGS could have offered finer resolution than MLST.", "cidm_contribution": "Direct CIDM Molecular Mycology involvement through Wieland Meyer and colleagues; strong One Health/environmental molecular epidemiology contribution.", "contradictions_unknowns": "Why only one of nine ferrets developed clinical disease despite shared exposure remains unresolved.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6900720/" }, { "review_event_id": "IRD-20261003-B02-06", "object_id": "CIDM-WORK-1800", "pmid": "31534685", "year": 2019, "title": "The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Environmental mycobiome study", "research_question": "Is the presence of pathogenic Cryptococcus in Australian tree hollows associated with a distinctive surrounding fungal community?", "methods_summary": "Twenty-three Australian tree hollows were studied using both culture and amplicon-based metagenomic sequencing to characterise fungal communities and Cryptococcus occurrence.", "main_finding": "No single fungal genus showed a clear correlation with Cryptococcus presence. Culture and NGS detected partly different signals and were best interpreted as complementary methods. The known environmental niche of pathogenic Cryptococcus was expanded to additional tree species.", "limitations": "Small number of tree hollows; amplicon sequencing has taxonomic and abundance biases; association does not establish ecological dependence.", "cidm_contribution": "Direct CIDM Molecular Mycology affiliation; extends environmental ecology and surveillance of Cryptococcus.", "contradictions_unknowns": "The ecological conditions that permit Cryptococcus persistence in some hollows remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31534685/" }, { "review_event_id": "IRD-20261003-B02-07", "object_id": "CIDM-WORK-1801", "pmid": "31167945", "year": 2019, "title": "Jet-Setting Koalas Spread Cryptococcus gattii VGII in Australia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular epidemiology / One Health investigation", "research_question": "Did movement of captive koalas introduce and disseminate C. gattii VGII into eastern Australian captive environments?", "methods_summary": "Investigation of a captive-koala disease cluster using clinical/environmental sampling, URA5 typing, MLST and WGS.", "main_finding": "Genomic and epidemiological evidence supported introduction of VGII from Western Australia and subsequent spread between eastern facilities through koala movements, consistent with a founder event.", "limitations": "Observational outbreak reconstruction; environmental persistence and exact transmission timing cannot be proven experimentally.", "cidm_contribution": "Direct CIDM Molecular Mycology involvement; links pathogen genomics, animal movement and environmental dissemination.", "contradictions_unknowns": "The degree to which introduced VGII competes with endemic VGI and the longer-term environmental persistence remain open.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31167945/" }, { "review_event_id": "IRD-20261003-B02-08", "object_id": "CIDM-WORK-1802", "pmid": "30269696", "year": 2019, "title": "Accurate identification of Australian mosquitoes using protein profiling", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic/taxonomic method validation", "research_question": "Can MALDI-TOF MS provide rapid and accurate identification of Australian mosquitoes?", "methods_summary": "Three hundred mosquitoes representing 21 species were morphologically identified; legs were analysed by MALDI-TOF MS, with a subset also tested by cox1 sequencing.", "main_finding": "The study established a reference MALDI-TOF MS spectra database and showed accurate identification of Australian mosquito species, including distinction of some closely related taxa that cox1 barcoding did not resolve.", "limitations": "Reference library size and geographic sampling constrain transferability; performance depends on specimen quality and database coverage.", "cidm_contribution": "Verified CIDM core-person lineage through Cameron E Webb; relevant to vector surveillance and mosquito-borne disease preparedness.", "contradictions_unknowns": "Performance across wider Australian mosquito diversity and routine surveillance workflows needs broader validation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30269696/" }, { "review_event_id": "IRD-20261003-B02-09", "object_id": "CIDM-WORK-1803", "pmid": "31619762", "year": 2020, "title": "Impact of chemokine C-C ligand 27, foreskin anatomy and sexually transmitted infections on HIV-1 target cell availability in adolescent South African males", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Human tissue immunology / mechanistic study", "research_question": "How do foreskin compartment, CCL27 expression and asymptomatic STIs affect the distribution of HIV target cells in adolescent males?", "methods_summary": "Foreskin tissue from adolescents undergoing medical circumcision was analysed for chemokine expression, CD4/CCR5 T cells, Langerhans cells, STI status and ex-vivo CCL27-induced T-cell migration.", "main_finding": "CCL27 was markedly higher in inner foreskin; HIV target cells were enriched near epithelial surfaces, especially with STIs. Exogenous CCL27 promoted migration of CD4 T cells into inner foreskin epithelium.", "limitations": "Small STI-positive sample size; tissue/ex-vivo findings do not directly measure HIV acquisition; causality for CCL27 in vivo remains incompletely established.", "cidm_contribution": "Verified CIDM person David A Lewis within the STI/HIV collaboration; connects STI biology with mechanisms of HIV susceptibility.", "contradictions_unknowns": "Whether CCL27 modulation materially changes real-world HIV acquisition risk remains unknown.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6914668/" }, { "review_event_id": "IRD-20261003-B02-10", "object_id": "CIDM-WORK-1804", "pmid": "30760230", "year": 2019, "title": "Macrolide and fluoroquinolone resistance-associated mutations in Mycoplasma genitalium in Johannesburg, South Africa, 2007-2014", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Retrospective molecular resistance surveillance", "research_question": "What resistance-associated mutations were present in M. genitalium in Johannesburg during 2007–2014, and were they associated with HIV status?", "methods_summary": "Stored M. genitalium-positive specimens were tested for 23S rRNA and quinolone-resistance-region mutations.", "main_finding": "No macrolide resistance-associated mutations were detected; one parC D87Y mutation linked to fluoroquinolone failure was found, while P62S was common but of uncertain significance. No clear association with HIV status was identified.", "limitations": "Retrospective stored specimens from earlier years; mutation-to-clinical-resistance correlations are incomplete; findings may not reflect current resistance prevalence.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes antimicrobial-resistance surveillance and STI laboratory epidemiology.", "contradictions_unknowns": "Resistance patterns may have changed substantially after wider azithromycin exposure; contemporary surveillance is required.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30760230/" }, { "review_event_id": "IRD-20261003-B02-11", "object_id": "CIDM-WORK-1805", "pmid": "30773651", "year": 2019, "title": "Early initiation of antiretroviral therapy for people newly diagnosed with HIV infection in Australia: trends and predictors, 2004-2015", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Retrospective multicentre cohort", "research_question": "How did early ART initiation change in Australia from 2004–2015 and what patient factors predicted treatment within six months of diagnosis?", "methods_summary": "Retrospective longitudinal data from 44 sexual-health clinics in the ACCESS network; 917 newly diagnosed people with HIV were analysed.", "main_finding": "Early ART increased from 17% in 2004–06 to 53% in 2013–15. Earlier treatment was associated with more recent calendar period, lower CD4 count and higher viral load.", "limitations": "Clinic-based observational data; practice patterns and guidelines evolved over time; does not by itself establish effects of earlier treatment on transmission or morbidity.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes Australian HIV care implementation and treatment-timing evidence.", "contradictions_unknowns": "How rapidly universal-treatment policy closed residual delays after 2015 is outside this study.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30773651/" }, { "review_event_id": "IRD-20261003-B02-12", "object_id": "CIDM-WORK-1806", "pmid": "30947260", "year": 2019, "title": "Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Cross-sectional genital immunology/microbiome study", "research_question": "What biological features define genital health in HIV-negative South African adolescent girls and young women at high HIV risk?", "methods_summary": "Cross-sectional assessment of 298 participants from Cape Town and Soweto including pH, bacterial vaginosis, STIs, microbiota sequencing, genital cytokines and cervical T-cell activation.", "main_finding": "The study showed that conventional 'normal' genital-health definitions based on low pH and Lactobacillus dominance do not fully describe this population; geography and biological factors were associated with substantial variation in microbiota and mucosal immune state.", "limitations": "Cross-sectional design; population- and geography-specific findings; associations cannot establish causal effects on HIV acquisition.", "cidm_contribution": "Verified CIDM person David A Lewis; integrates STI epidemiology with genital microbiology and HIV-susceptibility research.", "contradictions_unknowns": "Which microbiome/immune profiles are protective versus simply population-specific remains unresolved.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30947260/" }, { "review_event_id": "IRD-20261003-B02-13", "object_id": "CIDM-WORK-1807", "pmid": "31008842", "year": 2019, "title": "Serological Markers for Syphilis Among Persons Presenting With Syndromes Associated With Sexually Transmitted Infections: Results From the Zimbabwe STI Etiology Study", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Sentinel cross-sectional seroepidemiology", "research_question": "What is the prevalence of serological syphilis markers among patients presenting with common STI syndromes in Zimbabwe?", "methods_summary": "Regionally diverse clinic participants with genital ulcer disease, vaginal discharge or urethral discharge underwent RPR and TPHA testing.", "main_finding": "Overall 8.3% were positive on both RPR and TPHA, with highest positivity among women and men presenting with genital ulcer disease.", "limitations": "Syndromic sentinel population is not representative of the general population; serology cannot fully distinguish all stages or timing of infection.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes STI surveillance and syndromic-management evidence.", "contradictions_unknowns": "Population-level trends and the impact of expanded testing/treatment require ongoing surveillance.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31008842/" }, { "review_event_id": "IRD-20261003-B02-14", "object_id": "CIDM-WORK-1808", "pmid": null, "year": 2019, "title": "Vaginal microbiota varies by geographical location in South African women", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Cross-sectional microbiome comparison", "research_question": "Does vaginal microbial composition differ by geographic location among young Black South African women from Cape Town and Johannesburg?", "methods_summary": "16S rRNA amplicon sequencing of lateral vaginal wall swabs from women aged 16–22, with ecological comparisons incorporating geography, BMI, HPV risk and STI status.", "main_finding": "Geographic location was significantly associated with vaginal microbiota composition, alongside BMI and HPV risk, indicating that location/population context should be considered when defining vaginal microbiome patterns.", "limitations": "Cross-sectional observational design; geography may proxy unmeasured behavioural, environmental or socioeconomic factors; no PubMed record in the current corpus.", "cidm_contribution": "Verified CIDM person David A Lewis; links STI/HIV research with geographic variation in genital microbiota.", "contradictions_unknowns": "The causal drivers of geographic microbiome differences and their independent effect on HIV/STI risk remain uncertain.", "confidence": "MEDIUM", "source_url": "https://www.satnt.ac.za/index.php/satnt/article/view/685" }, { "review_event_id": "IRD-20261003-B02-15", "object_id": "CIDM-WORK-1809", "pmid": "31181033", "year": 2019, "title": "Performance of a Dual Human Immunodeficiency Virus/Syphilis Rapid Test Compared With Conventional Serological Testing for Syphilis and Human Immunodeficiency Virus in a Laboratory Setting: Results From the Zimbabwe STI Etiology Study", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic performance study", "research_question": "How accurately does a dual HIV/syphilis rapid test perform relative to conventional laboratory testing in specimens from Zimbabwe STI clinics?", "methods_summary": "Serum specimens from a multicentre STI aetiology study were tested with the SD Bioline HIV/Syphilis Duo; syphilis was compared with TPHA/RPR and HIV with the national laboratory testing algorithm.", "main_finding": "The dual rapid-test approach showed strong laboratory performance for combined HIV/syphilis screening and supports point-of-care use to expand testing in high-risk populations.", "limitations": "Laboratory performance may exceed field performance; specimen type, operator conditions and disease stage can affect sensitivity, particularly for syphilis.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes diagnostic implementation evidence for integrated STI/HIV testing.", "contradictions_unknowns": "Real-world impact on linkage to treatment, repeat testing and congenital-syphilis prevention requires implementation studies.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31181033/" }, { "review_event_id": "IRD-20261003-B02-16", "object_id": "CIDM-WORK-1810", "pmid": "31292063", "year": 2019, "title": "New treatment options for Neisseria gonorrhoeae in the era of emerging antimicrobial resistance", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Narrative therapeutic review", "research_question": "What treatment options may preserve or replace ceftriaxone-based therapy as gonococcal antimicrobial resistance increases?", "methods_summary": "Narrative review of existing and investigational agents, susceptibility-guided treatment and recent clinical-trial evidence.", "main_finding": "Ceftriaxone remained the mainstay. Precision susceptibility testing and selected repurposed drugs may help conserve it. Solithromycin and delafloxacin had disappointing trial results; zoliflodacin and gepotidacin were promising but oropharyngeal failures raised concerns about monotherapy.", "limitations": "Evidence landscape was rapidly evolving; conclusions predate later phase-3 and surveillance data; review rather than systematic meta-analysis.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes gonorrhoea AMR treatment strategy and translational STI expertise.", "contradictions_unknowns": "Durability of activity, resistance emergence and efficacy at the oropharyngeal site remain key uncertainties.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31292063/" }, { "review_event_id": "IRD-20261003-B02-17", "object_id": "CIDM-WORK-1811", "pmid": "31289109", "year": 2019, "title": "Disentangling the tangled web of Neisseria gonorrhoeae transmission: how important are oropharyngeal infections?", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Commentary/editorial", "research_question": "How important is the oropharynx in sustaining transmission of N. gonorrhoeae?", "methods_summary": "Commentary/editorial; PubMed provides no abstract.", "main_finding": "The article highlights the potential importance of oropharyngeal infection in gonorrhoea transmission and antimicrobial-resistance dynamics.", "limitations": "No abstract and no primary dataset in the PubMed record; interpretive commentary rather than new experimental evidence.", "cidm_contribution": "Verified CIDM person David A Lewis; contributes STI transmission and AMR interpretation.", "contradictions_unknowns": "The quantitative contribution of oropharyngeal infection to population transmission remains difficult to estimate.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31289109/" }, { "review_event_id": "IRD-20261003-B02-18", "object_id": "CIDM-WORK-1812", "pmid": "30903006", "year": 2019, "title": "Interactions of an Emerging Fungal Pathogen Scedosporium aurantiacum with Human Lung Epithelial Cells", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "In-vitro host-pathogen interaction study", "research_question": "How does S. aurantiacum interact with human lung epithelial cells during early infection?", "methods_summary": "A549 lung epithelial cells were co-cultured with a virulent S. aurantiacum strain; microscopy assessed attachment/germination and transcriptomics measured host-cell responses.", "main_finding": "Most conidia attached within four hours and germinated; host transcriptional responses showed inflammatory and repair pathways, including innate immune/NF-kB activation.", "limitations": "A549 monoculture is an in-vitro model and cannot reproduce the multicellular lung or immune environment; single fungal strain limits generalisability.", "cidm_contribution": "Direct CIDM Molecular Mycology affiliation through Wieland Meyer; contributes mechanistic fungal-pathogenesis evidence.", "contradictions_unknowns": "How these epithelial responses relate to invasion, persistence and disease severity in patients remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30903006/" }, { "review_event_id": "IRD-20261003-B02-19", "object_id": "CIDM-WORK-1813", "pmid": "31061785", "year": 2019, "title": "Cryptococcosis due to Cryptococcus gattii VGII in southeast Brazil: The One Health approach revealing a possible role for domestic cats", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Veterinary case report / One Health signal", "research_question": "Do feline C. gattii VGII infections in southeast Brazil signal local emergence of this molecular type in an area better known for C. neoformans VNI?", "methods_summary": "Two feline cryptococcosis cases were characterised by molecular typing and MLST.", "main_finding": "Both cats had C. gattii VGII with distinct sequence types, raising concern that VGII may be emerging in southeast Brazil and that domestic animals may provide One Health surveillance signals.", "limitations": "Only two cases; no environmental sampling proving local reservoirs; cannot estimate prevalence or direction of transmission.", "cidm_contribution": "Verified CIDM Molecular Mycology person Wieland Meyer; contributes molecular typing and One Health surveillance.", "contradictions_unknowns": "Whether these cases represent sustained local transmission or sporadic introductions remains unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/31061785/" }, { "review_event_id": "IRD-20261003-B02-20", "object_id": "CIDM-WORK-1814", "pmid": "30991682", "year": 2019, "title": "Clonal Dispersal of Cryptococcus gattii VGII in an Endemic Region of Cryptococcosis in Colombia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular epidemiology / phenotypic virulence study", "research_question": "What are the genetic and phenotypic characteristics of C. gattii VGII isolates in the endemic Cúcuta region of Colombia?", "methods_summary": "MLST, phenotypic characterisation, mating analysis, extracellular-enzyme assays and a mouse virulence model were used on Colombian isolates and compared with representative outbreak strains.", "main_finding": "Cúcuta isolates were highly clonal, predominantly ST25, with shared phenotypes, frequent mating type a and substantial virulence, supporting concern about clonal dissemination of potentially virulent strains.", "limitations": "Regional isolate set and animal model; observed virulence does not directly quantify human clinical risk or incidence.", "cidm_contribution": "Direct CIDM Molecular Mycology affiliation through Wieland Meyer; strengthens international cryptococcal molecular epidemiology.", "contradictions_unknowns": "Drivers of clonal spread and the relationship between laboratory virulence phenotypes and human outbreak risk remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30991682/" }, { "review_event_id": "IRD-20261003-B03-01", "object_id": "CIDM-WORK-1815", "pmid": "30953839", "year": 2019, "title": "Genotypes and population genetics of Cryptococcus neoformans and Cryptococcus gattii species complexes in Europe and the Mediterranean area", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Multicentre molecular epidemiology / population genetics", "research_question": "What genotypes and population structures characterize C. neoformans and C. gattii species complexes across Europe and the Mediterranean?", "methods_summary": "476 clinical and environmental isolates were analysed by multilocus sequence typing with phylogenetic and population-genetic analyses.", "main_finding": "VNI isolates showed a large clonal component dominated by ST23, whereas VNIV was more genetically heterogeneous. European C. gattii isolates were few and environmentally derived, clustering with a Mediterranean endemic lineage.", "limitations": "Sampling was geographically and source uneven; C. gattii numbers were small; MLST has lower resolution than whole-genome sequencing.", "cidm_contribution": "Verified CIDM Molecular Mycology contribution through Wieland Meyer; strengthens international cryptococcal population-genetic surveillance.", "contradictions_unknowns": "Fine-scale transmission and importation versus local persistence require higher-resolution genomic and longitudinal sampling.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30953839/" }, { "review_event_id": "IRD-20261003-B03-02", "object_id": "CIDM-WORK-1816", "pmid": "30649397", "year": 2019, "title": "Prevalence of cryptococcal antigenemia and nasal colonization in a free-ranging koala population", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Field prevalence / One Health surveillance", "research_question": "How common are cryptococcal antigenemia and nasal colonization in free-ranging koalas, and what host/environment factors are associated with them?", "methods_summary": "181 free-ranging koalas were tested by cryptococcal antigen lateral-flow assay and nasal culture; 14 eucalypts were also cultured and isolates were typed.", "main_finding": "Antigenemia occurred in 5.5% and nasal colonization in 6.6%; most isolates were C. gattii VGI. Colonized koalas were more likely to be antigen-positive, but most measured host/environment characteristics were not clearly associated.", "limitations": "Single regional population; relatively few antigen/colonization positives; limited environmental-tree sampling reduces power for risk-factor inference.", "cidm_contribution": "Direct CIDM Molecular Mycology affiliation; demonstrates wildlife sentinel value and expands cryptococcal ecological surveillance.", "contradictions_unknowns": "The apparent association with Eucalyptus camaldulensis abundance and the determinants of progression from colonization to disease remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30649397/" }, { "review_event_id": "IRD-20261003-B03-03", "object_id": "CIDM-WORK-1817", "pmid": "30916306", "year": 2019, "title": "Oviposition Behavior of Culex annulirostris (Diptera: Culicidae) Is Affected by the Recent Presence of Invasive Gambusia holbrooki (Cyprinodontiformes: Poeciliidae)", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Laboratory behavioural ecology experiment", "research_question": "Can Culex annulirostris detect and avoid water from wetlands recently containing the invasive fish Gambusia holbrooki?", "methods_summary": "Water from managed fish-reduction wetlands and adjacent fish-rich wetlands was tested in laboratory oviposition experiments on two occasions.", "main_finding": "Mosquitoes avoided water derived from fish-containing habitats even when fish were absent, indicating that recent predator presence can shape oviposition behaviour.", "limitations": "Laboratory choice assays may not fully represent field oviposition; chemical cues were not identified; only a limited temporal sampling was used.", "cidm_contribution": "Verified CIDM/NSW Health Pathology medical-entomology lineage through Cameron Webb; directly informs urban-wetland mosquito-risk management.", "contradictions_unknowns": "How long predator-associated cues persist and how strongly they alter field mosquito abundance remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30916306/" }, { "review_event_id": "IRD-20261003-B03-04", "object_id": "CIDM-WORK-1818", "pmid": "30858050", "year": 2019, "title": "Out-of-Africa, human-mediated dispersal of the common cat flea, Ctenocephalides felis: The hitchhiker's guide to world domination", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Global phylogeography / niche modelling", "research_question": "What is the evolutionary origin and global population structure of the common cat flea, and how has human-associated animal movement shaped its spread?", "methods_summary": "A global collection of >5,000 fleas was evaluated morphologically and genetically; multigene phylogenetics and cox1 data from 56 countries were combined with ecological niche modelling.", "main_finding": "The genus showed an African origin and C. felis displayed substantial genetic diversity partitioned into four bioclimatic clusters. Human movement of cats and dogs likely facilitated worldwide expansion.", "limitations": "Sampling density differed across regions and hosts; phylogeographic inference depends on marker resolution and current distributions; historical dispersal cannot be observed directly.", "cidm_contribution": "Medical-entomology contribution through Cameron Webb and NSW Health Pathology; relevant to vector/ectoparasite surveillance and One Health.", "contradictions_unknowns": "The relative contributions of recent human movement versus older natural dispersal require denser genomic and historical sampling.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/30858050/" }, { "review_event_id": "IRD-20261003-B03-05", "object_id": "CIDM-WORK-1819", "pmid": "", "year": 2019, "title": "Habitat Traits Associated with Mosquito Risk and Aquatic Diversity in Urban Wetlands", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Urban wetland field ecology", "research_question": "Which wetland and surrounding-landscape traits are associated with mosquito risk and aquatic macroinvertebrate diversity in Sydney urban wetlands?", "methods_summary": "Adult mosquitoes and aquatic macroinvertebrates were sampled at 23 wetlands across greater Sydney and related to habitat, wetland design and surrounding land use.", "main_finding": "Overall mosquito assemblages were not simply related to macroinvertebrate diversity or wetland design, although individual mosquito species showed specific associations. Macroinvertebrate diversity related more to surrounding land use and wetland design than to available aquatic habitat.", "limitations": "Observational ecological associations; seasonal/site variability and species-specific responses limit simple generalisation.", "cidm_contribution": "Cameron Webb medical-entomology lineage; supports evidence-based balancing of biodiversity benefits and mosquito public-health risk.", "contradictions_unknowns": "Which design interventions optimise biodiversity while suppressing the highest-risk mosquito species requires prospective intervention studies.", "confidence": "HIGH", "source_url": "https://hero.epa.gov/reference/6708025/" }, { "review_event_id": "IRD-20261003-B03-06", "object_id": "CIDM-WORK-1820", "pmid": "", "year": 2019, "title": "The application of Geographic Information System (GIS) to assess the population abundance of Aedes albopictus (Skuse) in mangrove forests of Penang, Malaysia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Vector-surveillance / GIS field study", "research_question": "Can ovitrap surveillance integrated with GIS map Aedes albopictus abundance and potential vector risk in a difficult-to-survey mangrove environment?", "methods_summary": "Ovitrap data collected over six months in Pulau Betong mangrove habitat were spatially mapped using GIS to describe abundance and temporal distribution.", "main_finding": "Aedes albopictus was widely detected with seasonal peaks, including higher activity around August and October before a marked decline with the dry season, showing that GIS-assisted surveillance can characterize spatial-temporal risk.", "limitations": "Single mangrove location and limited time series; ovitrap counts are proxies for population abundance and do not directly measure pathogen transmission.", "cidm_contribution": "Cameron Webb medical-entomology collaboration; extends vector-surveillance methods into challenging tropical habitats.", "contradictions_unknowns": "How well GIS/ovitrap abundance predicts human biting or pathogen-transmission risk remains uncertain.", "confidence": "MEDIUM", "source_url": "https://www.dipterajournal.com/pdf/2019/vol6issue1/PartA/6-1-7-887.pdf" }, { "review_event_id": "IRD-20261003-B03-07", "object_id": "CIDM-WORK-1821", "pmid": "", "year": 2019, "title": "Engaging urban stakeholders in the sustainable management of arthropod pests", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Narrative review / urban integrated pest management", "research_question": "Why is integrated pest management underused in cities and what stakeholder strategies could improve sustainable urban arthropod control?", "methods_summary": "Narrative synthesis comparing urban and agricultural pest management, summarising examples of successful IPM and barriers to adoption.", "main_finding": "Urban pest control remains overly dependent on chemical control. Major barriers to IPM include diverse stakeholder interests, limited awareness, insufficient monitoring, resource constraints, public perceptions and policy settings; stakeholder engagement and implementation support are central solutions.", "limitations": "Narrative rather than systematic review; evidence quality and applicability of examples vary by pest and jurisdiction.", "cidm_contribution": "Cameron Webb contribution links medical entomology to sustainable urban pest-management practice and community engagement.", "contradictions_unknowns": "Which stakeholder interventions deliver durable reductions in pesticide reliance at city scale needs empirical implementation testing.", "confidence": "HIGH", "source_url": "https://researchers.mq.edu.au/en/publications/engaging-urban-stakeholders-in-the-sustainable-management-of-arth/" }, { "review_event_id": "IRD-20261003-B03-08", "object_id": "CIDM-WORK-1822", "pmid": "", "year": 2019, "title": "Clean bill of health? Towards an understanding of health risks posed by urban ibis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Urban wildlife pathogen surveillance", "research_question": "Do urban Australian White Ibis in Sydney represent important reservoirs or sentinels for arboviruses and Salmonella?", "methods_summary": "72 ibis at two urban sites were sampled in 2003 and 2015 for arbovirus antibodies and Salmonella shedding.", "main_finding": "One 2015 ibis showed evidence of prior WNV-Kunjin exposure; no other flavivirus signals were found. Salmonella was undetected in 2015 but had been found in 25% in 2003. Results favour a sentinel role over a clear major reservoir role.", "limitations": "Small sample, two sites and two discrete time points; serology reflects past exposure and cannot establish local transmission source.", "cidm_contribution": "Cameron Webb medical-entomology collaboration; bridges wildlife, arbovirus surveillance and urban public-health risk.", "contradictions_unknowns": "WNV-Kunjin host competence of ibis and reasons for large temporal differences in Salmonella detection remain unresolved.", "confidence": "HIGH", "source_url": "https://academic.oup.com/jue/article/5/1/juz006/5506280" }, { "review_event_id": "IRD-20261003-B03-09", "object_id": "CIDM-WORK-1823", "pmid": "31801896", "year": 2020, "title": "Team huddles in sexual health clinics improve communication, clinic capacity and flow, and team relationships and well-being", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Quality-improvement research letter", "research_question": "Are brief daily team huddles feasible and perceived as beneficial in an outpatient sexual-health/HIV clinic?", "methods_summary": "A daily clinical-administrative huddle was introduced; after three months, 22 of 26 staff completed a brief anonymous survey with Likert ratings and free-text feedback.", "main_finding": "Staff highly valued huddles and reported improvements in communication, clinic capacity/flow, team relationships and well-being, with no barriers reported in this small quality-improvement evaluation.", "limitations": "Single clinic, small self-reported survey, no control group and no objective patient-safety or throughput endpoints.", "cidm_contribution": "David A Lewis / Western Sydney Sexual Health lineage; operational health-services contribution to sexual-health care delivery.", "contradictions_unknowns": "Whether perceived benefits translate into measurable safety, efficiency or patient outcomes requires controlled evaluation.", "confidence": "HIGH", "source_url": "https://sti.bmj.com/content/96/4/312" }, { "review_event_id": "IRD-20261003-B03-10", "object_id": "CIDM-WORK-1824", "pmid": "31907328", "year": 2020, "title": "Clinical characteristics of overseas-born men who have sex with men (MSM) in the AHOD cohort and implications for clinical practice", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Observational cohort analysis / research letter", "research_question": "Once in HIV care, do overseas-born MSM have different virological treatment responses compared with Australian-born MSM?", "methods_summary": "AHOD data were analysed for time to virological suppression and subsequent virological failure, including overseas-born subgroups and adjustment for clinical and treatment variables.", "main_finding": "After adjustment, overseas-born MSM did not differ significantly from Australian-born MSM in rate of virological suppression or first virological failure, suggesting major disparities may occur before or at entry to care rather than treatment response once engaged.", "limitations": "Observational cohort; overseas-born status is heterogeneous; cohort participation and healthcare access may select for people already engaged in care.", "cidm_contribution": "David A Lewis CIDM/Westmead contribution; informs HIV clinical equity and culturally diverse care.", "contradictions_unknowns": "Barriers to diagnosis, ART initiation and retention before AHOD enrolment remain outside the analysis.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7335683/" }, { "review_event_id": "IRD-20261003-B03-11", "object_id": "CIDM-WORK-1825", "pmid": "31911427", "year": 2020, "title": "On-demand HIV pre-exposure prophylaxis: what are the healthcare workers' barriers to delivery in a culturally and linguistically diverse population?", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Healthcare-worker survey / research letter", "research_question": "What barriers do experienced sexual-health workers perceive when discussing and delivering on-demand PrEP to a culturally diverse MSM population?", "methods_summary": "Healthcare workers in Western Sydney Sexual Health Centre were surveyed about barriers and confidence regarding on-demand PrEP.", "main_finding": "Staff reported uncertainty about guidelines, perceived complexity of the dosing schedule and insufficient evidence; 15 of 17 (88%) wanted more training, indicating a specific implementation gap despite experience with daily PrEP.", "limitations": "Very small single-centre staff survey; attitudes may change rapidly as guidelines and evidence evolve.", "cidm_contribution": "David A Lewis / Western Sydney sexual-health lineage; implementation evidence for equitable PrEP delivery.", "contradictions_unknowns": "Whether targeted training improves actual on-demand PrEP uptake, adherence and outcomes in culturally diverse populations needs evaluation.", "confidence": "HIGH", "source_url": "https://sti.bmj.com/content/96/7/549" }, { "review_event_id": "IRD-20261003-B03-12", "object_id": "CIDM-WORK-1826", "pmid": "32168465", "year": 2020, "title": "Epidemiology of Coronavirus Disease in Gansu Province, China, 2020", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Early outbreak epidemiology / spatial analysis", "research_question": "What were the epidemiological and spatial characteristics of early COVID-19 cases in Gansu Province, distant from Wuhan?", "methods_summary": "Early reported cases were characterised by exposure, demographics, timing and transport; family-cluster timing and spatial hot spots/outliers were analysed.", "main_finding": "Most early cases were imported, with epidemiological differences between first and second waves. Shorter delays to care/hospitalisation and public-health interventions coincided with decreasing transmission.", "limitations": "Early-pandemic small case series; case ascertainment, testing capacity and rapidly changing interventions limit causal inference about control effectiveness.", "cidm_contribution": "Mark W Douglas collaboration; contributes early international outbreak epidemiology and public-health response analysis.", "contradictions_unknowns": "The relative contribution of individual interventions versus changing importation pressure cannot be separated.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32168465/" }, { "review_event_id": "IRD-20261003-B03-13", "object_id": "CIDM-WORK-1827", "pmid": "32193545", "year": 2021, "title": "A pilot study: the influence of staff attitudes and beliefs on managing contacts of sexually transmitted infections", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Pilot letter", "research_question": "How might staff attitudes and beliefs influence STI contact-management practice?", "methods_summary": "Pilot/letter format; PubMed supplies no abstract in the current source-return.", "main_finding": "The article addresses behavioural and attitudinal determinants of partner/contact management among sexual-health staff.", "limitations": "No attributable abstract retrieved in this pass; detailed methods, sample size and quantitative findings are not represented here.", "cidm_contribution": "David A Lewis / Western Sydney Sexual Health collaboration; relevant to implementation quality in partner notification.", "contradictions_unknowns": "Specific attitude-outcome relationships require full-text return before deeper conclusions are justified.", "confidence": "LOW", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32193545/" }, { "review_event_id": "IRD-20261003-B03-14", "object_id": "CIDM-WORK-1828", "pmid": "32228828", "year": 2020, "title": "Prevalence of sexually transmissible infections and HIV in men attending sex-on-premises venues in Australia: a systematic review and meta-analysis of observational studies", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Systematic review and meta-analysis", "research_question": "What are pooled STI and HIV prevalence estimates among men tested at Australian sex-on-premises venues?", "methods_summary": "Twelve cross-sectional studies of on-site testing (2000–2017) were synthesised, with pooled prevalence estimates by infection/anatomical site.", "main_finding": "Pooled prevalence was substantial: CT ~3.4%, NG ~1.3%, HIV ~2.3% and syphilis ~3.2%, with anatomical-site differences. The studies predated broad PrEP uptake.", "limitations": "High heterogeneity, variable participation and testing strategies; pre-PrEP evidence may not represent current epidemiology.", "cidm_contribution": "David A Lewis contribution; supports targeted sexual-health outreach and surveillance in high-risk settings.", "contradictions_unknowns": "How PrEP-era behavioural and testing changes affect contemporary SOPV prevalence requires updated studies.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32228828/" }, { "review_event_id": "IRD-20261003-B03-15", "object_id": "CIDM-WORK-1829", "pmid": "32229546", "year": 2021, "title": "HBV vaccination and HBV infection induces HBV-specific natural killer cell memory", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human immunology / mechanistic study", "research_question": "Does human HBV vaccination or chronic infection generate antigen-specific memory-like NK-cell responses?", "methods_summary": "NK-cell responses from vaccinated, unvaccinated and chronic-HBV participants were tested against HBV antigen-pulsed autologous dendritic cells using cytotoxicity, proliferation and degranulation assays.", "main_finding": "Vaccinated participants showed enhanced HBsAg-specific NK responses, and chronic-HBV participants showed HBcAg-reactive NK responses. Memory-like activity was associated with mature CD56dim phenotypes and inversely correlated with HBV DNA in chronic infection.", "limitations": "Ex-vivo functional assays and selected cohorts; clinical protection or therapeutic efficacy from these NK responses is not established.", "cidm_contribution": "Mark W Douglas contribution; mechanistic HBV immunology with implications for vaccine biology and cure strategies.", "contradictions_unknowns": "Durability, clonal basis and causal contribution of memory NK cells to viral control remain open.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32229546/" }, { "review_event_id": "IRD-20261003-B03-16", "object_id": "CIDM-WORK-1830", "pmid": "32234962", "year": 2020, "title": "Primary syphilis in men causes painful anogenital lesions and serology is not always helpful", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Clinical short report / letter", "research_question": "How reliably do classical symptom expectations and serology identify primary syphilis in men with anogenital lesions?", "methods_summary": "Short clinical publication; PubMed provides no abstract in this source-return.", "main_finding": "The title and indexing signal two practical messages: primary syphilis lesions can be painful, and serology may be negative or otherwise unhelpful early in infection.", "limitations": "No attributable abstract/full methods retrieved in this pass; exact sample size, diagnostic algorithm and effect estimates are not represented.", "cidm_contribution": "David A Lewis / Western Sydney Sexual Health contribution; clinically relevant diagnostic caution for syphilis.", "contradictions_unknowns": "Full-text return is required before quantifying lesion characteristics or serological sensitivity.", "confidence": "LOW", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32234962/" }, { "review_event_id": "IRD-20261003-B03-17", "object_id": "CIDM-WORK-1831", "pmid": "32392763", "year": 2020, "title": "The Lived Experience of Chronic Hepatitis B: A Broader View of Its Impacts and Why We Need a Cure", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Narrative review / patient-centred perspective", "research_question": "What psychosocial and societal harms of chronic hepatitis B are missed by a narrow clinical focus, and how could cure affect them?", "methods_summary": "Narrative synthesis of patient-experience, stigma, discrimination, economic and psychosocial literature with community perspectives.", "main_finding": "CHB imposes substantial lifelong psychosocial burdens including fear, stigma, discrimination, rejection and financial instability, which can themselves impede diagnosis and care. The review argues that cure would have value beyond prevention of cirrhosis/cancer.", "limitations": "Narrative evidence base with heterogeneous countries and measures; psychosocial benefit of future cure is partly inferential.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; extends HBV work from virology and treatment to patient-centred outcomes.", "contradictions_unknowns": "The magnitude of psychosocial improvement after functional cure and how best to measure it prospectively remain uncertain.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7290920/" }, { "review_event_id": "IRD-20261003-B03-18", "object_id": "CIDM-WORK-1832", "pmid": "32392852", "year": 2020, "title": "Indoor Dust as a Source of Virulent Strains of the Agents of Cryptococcosis in the Rio Negro Micro-Region of the Brazilian Amazon", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Environmental molecular epidemiology / virulence study", "research_question": "Can household dust in the Brazilian Amazon harbour genetically diverse and virulent Cryptococcus strains relevant to human exposure?", "methods_summary": "Indoor dust from homes was cultured; isolates underwent MLST and selected strains were assessed for virulence in Galleria mellonella.", "main_finding": "8.9% of houses were positive, yielding C. neoformans VNI and C. gattii VGII with multiple sequence types, including outbreak-associated genotypes. Several isolates showed virulence comparable to a highly virulent reference strain.", "limitations": "Household positivity does not establish human infection source; insect-model virulence may not translate directly to human disease; regional sampling.", "cidm_contribution": "Direct CIDM Molecular Mycology involvement; integrates environmental exposure, genotyping and virulence.", "contradictions_unknowns": "The actual risk attributable to chronic indoor-dust exposure and its link to clinical cases remains to be demonstrated.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32392852/" }, { "review_event_id": "IRD-20261003-B03-19", "object_id": "CIDM-WORK-1833", "pmid": "32403988", "year": 2020, "title": "Partner notification and treatment outcomes among South African adolescents and young adults diagnosed with a sexually transmitted infection via laboratory-based screening", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Prospective cohort / STI care cascade", "research_question": "After laboratory-diagnosed STI in South African youth, how often are treatment, partner notification and partner treatment completed?", "methods_summary": "AYAZAZI participants aged 16–24 underwent laboratory STI screening; diagnosed participants were followed for treatment, partner notification/treatment and recurrent infection.", "main_finding": "Among surveyed STI-positive participants, all reported completing treatment, 74% notified a partner, but only 35% reported partner treatment. Recurrent chlamydia occurred in a minority.", "limitations": "Small STI-positive sample and incomplete follow-up survey; partner treatment was self-reported; limited power to link notification to recurrence.", "cidm_contribution": "David A Lewis collaboration; contributes adolescent STI implementation and partner-management evidence.", "contradictions_unknowns": "How to convert high index-patient treatment into reliably treated partners remains a major implementation gap.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32403988/" }, { "review_event_id": "IRD-20261003-B03-20", "object_id": "CIDM-WORK-1834", "pmid": "32421299", "year": 2020, "title": "Factors Associated With Early Resumption of Condomless Anal Sex Among Men Who Have Sex With Men After Rectal Chlamydia Treatment", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Prospective behavioural analysis nested in treatment trial", "research_question": "How often do MSM resume condomless receptive anal sex soon after rectal chlamydia treatment, and which factors predict early resumption?", "methods_summary": "Participants in a rectal-chlamydia treatment trial reported weekly sexual behaviour for three weeks; regression identified factors associated with early resumption.", "main_finding": "About 9.5% resumed condomless receptive anal sex within one week. Current PrEP use and having many recent sexual partners were strongly associated with early resumption.", "limitations": "Behaviour was self-reported and drawn from trial participants; study does not directly demonstrate reinfection or antimicrobial resistance caused by early sex.", "cidm_contribution": "David A Lewis within the RTS investigator network; links behavioural epidemiology to STI treatment guidance.", "contradictions_unknowns": "The extent to which early resumption causes reinfection, onward transmission or selection pressure in routine care remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32421299/" }, { "review_event_id": "IRD-20261003-B04-01", "object_id": "CIDM-WORK-1835", "pmid": "32511709", "year": 2020, "title": "New multilocus sequence typing primers to enable genotyping of AD hybrids within the Cryptococcus neoformans species complex", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular typing method development", "research_question": "Can lineage-specific MLST primers overcome allele-amplification problems in C. neoformans AD hybrids?", "methods_summary": "New molecular-type-specific primers were designed and tested across the seven loci of the ISHAM consensus MLST scheme in haploid and hybrid strains.", "main_finding": "The primers specifically amplified VNI and VNIV alleles in diploid/aneuploid AD hybrids, enabling standardized MLST genotyping that had previously been difficult.", "limitations": "Method validation rather than epidemiological application; broader inter-laboratory reproducibility and use in diverse hybrid populations still require continued testing.", "cidm_contribution": "Direct CIDM Molecular Mycology contribution through Wieland Meyer; strengthens global Cryptococcus molecular epidemiology infrastructure.", "contradictions_unknowns": "The downstream gain in phylogenetic resolution and comparability across large hybrid collections remains to be demonstrated.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32511709/" }, { "review_event_id": "IRD-20261003-B04-02", "object_id": "CIDM-WORK-1836", "pmid": "32714773", "year": 2020, "title": "Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Conceptual review / taxonomy standards", "research_question": "How accurate is fungal DNA barcoding and what framework best supports reliable species identification?", "methods_summary": "Conceptual review of fungal identification, DNA barcoding, reference databases, taxonomy and verification practice, advocating integrative/polyphasic taxonomy.", "main_finding": "Single-marker barcoding alone can be insufficient; reliable fungal identification requires verified reference data and integration of phylogeny, phenotype/ecology and, when feasible, reproductive biology.", "limitations": "Review/framework paper; recommendations depend on taxonomic group and data availability and are not a single experimentally validated diagnostic algorithm.", "cidm_contribution": "CIDM Molecular Mycology contribution; directly relevant to reference databases, fungal diagnostics and quality assurance.", "contradictions_unknowns": "How to operationalize integrative taxonomy at scale in routine clinical laboratories remains an implementation challenge.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7353689/" }, { "review_event_id": "IRD-20261003-B04-03", "object_id": "CIDM-WORK-1837", "pmid": "32756480", "year": 2020, "title": "COVID-19: The Immune Responses and Clinical Therapy Candidates", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Early COVID-19 immunology/therapy review", "research_question": "What was known early in the pandemic about SARS-CoV-2 immune responses and candidate therapeutic strategies?", "methods_summary": "Narrative review synthesizing early evidence on innate/adaptive immunity, cytokine responses, antiviral candidates, immunomodulators and vaccine concepts.", "main_finding": "The review highlighted dysregulated inflammation alongside antiviral immune responses and surveyed then-emerging antiviral and immunomodulatory approaches.", "limitations": "Published early in the pandemic; many therapeutic candidates and mechanistic interpretations were provisional and later evidence changed clinical practice substantially.", "cidm_contribution": "CIDM-linked COVID-19 synthesis relevant to infectious-disease intelligence during an emerging outbreak.", "contradictions_unknowns": "Early-pandemic therapeutic ranking should not be treated as current guidance; later randomized evidence supersedes many candidate assumptions.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32756480/" }, { "review_event_id": "IRD-20261003-B04-04", "object_id": "CIDM-WORK-1838", "pmid": "32777077", "year": 2021, "title": "Hepatitis C Virus (HCV) Eradication With Interferon-Free Direct-Acting Antiviral-Based Therapy Results in KLRG1+ HCV-Specific Memory Natural Killer Cells", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human immunology / longitudinal treatment study", "research_question": "Does DAA-mediated HCV clearance generate persistent HCV-specific memory-like NK-cell responses?", "methods_summary": "NK-cell phenotypes and antigen-specific responses were compared before therapy and after sustained virological response in chronic HCV patients.", "main_finding": "After HCV cure, NK cells showed a more mature phenotype and stronger HCV-specific cytotoxic responses mediated by KLRG1+ NK cells, consistent with memory-like NK-cell formation.", "limitations": "Mechanistic ex-vivo study; protective significance, durability beyond observed follow-up and generalizability require further work.", "cidm_contribution": "Mark W Douglas / Westmead liver-immunology contribution; links antiviral cure to immune-memory biology.", "contradictions_unknowns": "Whether these memory-like NK cells improve protection against reinfection or have therapeutic utility is unknown.", "confidence": "HIGH", "source_url": "https://academic.oup.com/jid/article/223/7/1183/5890638" }, { "review_event_id": "IRD-20261003-B04-05", "object_id": "CIDM-WORK-1839", "pmid": "32784766", "year": 2020, "title": "Rearing and Maintenance of Galleria mellonella and Its Application to Study Fungal Virulence", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Methods review / protocol", "research_question": "How can Galleria mellonella be reared and standardized to improve reproducibility in fungal virulence studies?", "methods_summary": "Open-access methods review describing artificial diet, maintenance conditions and use of larvae in fungal virulence and gene-knockout experiments.", "main_finding": "Standardized in-house rearing can reduce stress and supplier-dependent variability, improving reproducibility of Galleria-based infection experiments.", "limitations": "Non-mammalian model; standardization recommendations are based partly on laboratory practice and do not remove biological differences from mammalian infection.", "cidm_contribution": "Direct CIDM Molecular Mycology methods contribution; supports reproducible fungal-pathogenesis experimentation.", "contradictions_unknowns": "Cross-laboratory standardization and the extent to which Galleria phenotypes predict mammalian virulence remain open.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7558789/" }, { "review_event_id": "IRD-20261003-B04-06", "object_id": "CIDM-WORK-1840", "pmid": "32824653", "year": 2020, "title": "Molecular Epidemiology Reveals Low Genetic Diversity among Cryptococcus neoformans Isolates from People Living with HIV in Lima, Peru, during the Pre-HAART Era", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Retrospective molecular epidemiology", "research_question": "What was the genetic diversity of C. neoformans causing disease in people with HIV in Lima before widespread HAART?", "methods_summary": "48 isolates from 20 HIV-positive patients were characterized using mating type, serotyping, RFLP, PCR fingerprinting, AFLP and MLST.", "main_finding": "The population showed low genetic diversity, dominated by VNI, with persistent infections often yielding the same genotype over follow-up.", "limitations": "Small retrospective pre-HAART collection; findings may not represent current strain diversity or contemporary treatment-era epidemiology.", "cidm_contribution": "Direct CIDM Molecular Mycology molecular-epidemiology expertise.", "contradictions_unknowns": "Whether low diversity reflects local transmission, sampling structure or historical treatment context requires broader genomic comparison.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7459599/" }, { "review_event_id": "IRD-20261003-B04-07", "object_id": "CIDM-WORK-1841", "pmid": "32844589", "year": 2020, "title": "Inconsistent HIV pre-exposure prophylaxis use and HIV transmission in men who have sex with men (MSM)", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Letter/commentary", "research_question": "What does inconsistent PrEP use imply for HIV transmission risk among MSM?", "methods_summary": "Commentary/letter linked to prior JIAS work; PubMed record does not provide a primary-study abstract.", "main_finding": "The publication emphasizes that inconsistent PrEP use remains a key pathway for preventable HIV transmission despite high effectiveness when PrEP is used appropriately.", "limitations": "Not a new primary dataset; conclusions are interpretive and depend on the commented-on evidence base.", "cidm_contribution": "David A Lewis / Western Sydney sexual-health contribution to PrEP implementation interpretation.", "contradictions_unknowns": "Full context should be read alongside the original study and reply; this review event does not treat the letter as independent efficacy evidence.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32844589/" }, { "review_event_id": "IRD-20261003-B04-08", "object_id": "CIDM-WORK-1842", "pmid": "32912933", "year": 2021, "title": "Mycoplasma genitalium coinfection in men with symptomatic gonococcal urethritis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Retrospective clinical epidemiology", "research_question": "How often is M. genitalium present in men with symptomatic gonococcal urethritis?", "methods_summary": "Retrospective analysis of symptomatic urethral gonorrhoea cases at Western Sydney Sexual Health Centre in 2017–2018.", "main_finding": "M. genitalium was detected in 14/184 men (7.6%), while chlamydia coinfection occurred in 15.8%; no clear demographic or behavioural predictors identified M. genitalium coinfection.", "limitations": "Single-centre retrospective study; symptomatic population only; coinfection prevalence may differ in other settings.", "cidm_contribution": "Direct Western Sydney/CIDM-linked STI diagnostic and clinical-epidemiology contribution.", "contradictions_unknowns": "Whether routine M. genitalium testing should accompany gonorrhoea diagnosis depends on local prevalence, resistance and treatment implications.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/32912933/" }, { "review_event_id": "IRD-20261003-B04-09", "object_id": "CIDM-WORK-1843", "pmid": "33143112", "year": 2020, "title": "Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Consensus molecular typing method", "research_question": "Can a standardized MLST scheme improve inter-study comparability for P. jirovecii molecular epidemiology?", "methods_summary": "International comparison and consensus work evaluated candidate loci and proposed a harmonized multilocus sequence-typing framework.", "main_finding": "The paper established a consensus MLST approach intended to reduce methodological heterogeneity and facilitate comparable P. jirovecii epidemiology across laboratories.", "limitations": "Sequence typing resolution depends on loci and sample quality; adoption across laboratories and performance against whole-genome methods remain ongoing issues.", "cidm_contribution": "Direct CIDM Molecular Mycology contribution through Wieland Meyer; infrastructure for fungal molecular epidemiology.", "contradictions_unknowns": "How broadly the scheme will be adopted and when WGS should supersede MLST remain open.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/33143112/" }, { "review_event_id": "IRD-20261003-B04-10", "object_id": "CIDM-WORK-1844", "pmid": "33176727", "year": 2020, "title": "Treating male partners of women with bacterial vaginosis (StepUp): a protocol for a randomised controlled trial to assess the clinical effectiveness of male partner treatment for reducing the risk of BV recurrence", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Randomized controlled trial protocol", "research_question": "Does concurrent treatment of male partners reduce recurrent bacterial vaginosis in women compared with treating women alone?", "methods_summary": "Open-label multicentre randomized trial protocol; couples randomized 1:1 to standard female treatment versus female plus male partner treatment, with 12-week follow-up.", "main_finding": "This is a protocol, not an outcome paper. It defines a trial designed to test whether targeting male carriage can reduce the high recurrence rate of BV.", "limitations": "No efficacy result should be inferred from the protocol; open-label design and adherence/tolerability are important implementation issues.", "cidm_contribution": "David A Lewis and STI research network contribution to partner-treatment strategy and BV recurrence research.", "contradictions_unknowns": "The protocol hypothesis required later trial results for confirmation; this record must remain linked to its outcome publications.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7661182/" }, { "review_event_id": "IRD-20261003-B04-11", "object_id": "CIDM-WORK-1845", "pmid": "33219381", "year": 2021, "title": "No Evidence That Salt Water Ingestion Kills Adult Mosquitoes (Diptera: Culicidae)", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Controlled laboratory survival experiment", "research_question": "Does ingestion of salt water reduce survival of adult mosquitoes as claimed by commercial/public sources?", "methods_summary": "Nine mosquito species were maintained for one week on water, sugar water, salt water or sugar-plus-salt diets under controlled conditions.", "main_finding": "Survival depended on sugar availability, not salt; the study found no evidence that salt ingestion kills adult mosquitoes.", "limitations": "Laboratory feeding conditions do not reproduce all field behaviours; the experiment tests the biological claim, not field-device effectiveness under every deployment scenario.", "cidm_contribution": "Cameron Webb medical-entomology contribution; directly addresses misinformation relevant to mosquito control.", "contradictions_unknowns": "Field trials of specific commercial devices could still assess attraction/capture effects, but the salt-toxicity claim itself lacked support here.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7954108/" }, { "review_event_id": "IRD-20261003-B04-12", "object_id": "CIDM-WORK-1846", "pmid": "34452444", "year": 2021, "title": "SHARED: An International Collaboration to Unravel Hepatitis C Resistance", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "International surveillance/network methods paper", "research_question": "Can an international pooled data platform improve understanding and harmonization of HCV antiviral resistance?", "methods_summary": "The SHARED consortium aggregates HCV sequences, patient data, regimen history and outcomes across laboratories, cohorts, trials and networks.", "main_finding": "The collaboration created a framework for harmonized resistance-associated-substitution interpretation, pooled prevalence/transmission analyses and shared tools that individual datasets could not support alone.", "limitations": "Network paper rather than a single clinical-effect estimate; data harmonization, representativeness and evolving resistance definitions remain challenges.", "cidm_contribution": "Mark W Douglas contribution connects Westmead HCV expertise to global antiviral-resistance surveillance.", "contradictions_unknowns": "Coverage gaps and biases across contributing countries/cohorts may influence resistance estimates.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/pmid/34452444/" }, { "review_event_id": "IRD-20261003-B04-13", "object_id": "CIDM-WORK-1847", "pmid": "34339277", "year": 2021, "title": "Demographic and Behavioral Risk Factors Associated with Reduced Susceptibility of Neisseria gonorrhoeae to First-Line Antimicrobials in South African Men with Gonococcal Urethral Discharge", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Sentinel antimicrobial-resistance epidemiology", "research_question": "Which demographic and behavioural factors are associated with gonococcal isolates showing resistance or reduced susceptibility to first-line antimicrobials in South African men?", "methods_summary": "685 men with gonococcal urethral discharge from sentinel surveillance clinics (2017–2019) were analysed for AMR phenotype and associated host/behavioural characteristics.", "main_finding": "The study identified epidemiological correlates of isolates with resistance/reduced susceptibility, supporting targeted AMR surveillance rather than assuming resistance is randomly distributed.", "limitations": "Sentinel symptomatic male population; observational associations cannot establish causes of resistance acquisition or transmission.", "cidm_contribution": "David A Lewis contribution; strengthens international gonococcal AMR surveillance and risk stratification.", "contradictions_unknowns": "Risk-factor profiles may change as resistance lineages and treatment practices evolve.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34339277/" }, { "review_event_id": "IRD-20261003-B04-14", "object_id": "CIDM-WORK-1848", "pmid": "34266538", "year": 2021, "title": "Barriers to HIV testing in hospital settings within a culturally diverse urban district of Sydney, Australia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Cross-sectional healthcare-worker survey", "research_question": "What prevents hospital health workers in culturally diverse Western Sydney from offering HIV testing?", "methods_summary": "420 health workers completed a survey on testing awareness, confidence and perceived barriers.", "main_finding": "Awareness and confidence were low outside doctors/midwives. Leading barriers included procedural knowledge, identifying at-risk patients, HIV knowledge, positive-result management and privacy/stigma concerns.", "limitations": "Only about 3% of the estimated workforce responded, creating substantial response-bias risk; attitudes do not equal observed testing behaviour.", "cidm_contribution": "Direct Western Sydney sexual-health implementation research through David A Lewis.", "contradictions_unknowns": "Whether targeted education changes actual hospital testing rates requires prospective intervention evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34266538/" }, { "review_event_id": "IRD-20261003-B04-15", "object_id": "CIDM-WORK-1849", "pmid": "34540311", "year": 2021, "title": "Prioritizing mosquito-borne diseases during and after the COVID-19 pandemic", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Public-health perspective", "research_question": "How should mosquito-borne disease prevention be protected when COVID-19 diverts public-health resources?", "methods_summary": "Perspective drawing on mosquito-borne disease epidemiology and pandemic service disruption.", "main_finding": "The paper argues that COVID-19 response should not displace vector surveillance and control because dengue and other mosquito-borne threats can continue or rebound during health-system disruption.", "limitations": "Perspective rather than controlled empirical study; recommendations are context dependent.", "cidm_contribution": "Cameron Webb medical-entomology contribution to pandemic-era vector-control policy.", "contradictions_unknowns": "The optimal allocation of constrained public-health resources across concurrent epidemics requires local burden and cost-effectiveness data.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8421746/" }, { "review_event_id": "IRD-20261003-B04-16", "object_id": "CIDM-WORK-1850", "pmid": "34011431", "year": 2021, "title": "Cross-sectional study of sexual behaviour and health of gay and bisexual men in suburban Sydney, New South Wales, Australia: contrasts between sex venue and clinic attendees", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Cross-sectional behavioural/clinical comparison", "research_question": "How do gay and bisexual men reached at a sex-on-premises venue differ from those attending a sexual-health clinic?", "methods_summary": "84 SOPV attendees and 108 sexual-health-clinic attendees completed behavioural questionnaires and HIV/STI testing.", "main_finding": "SOPV attendees were older and had lower prior HIV/STI testing and hepatitis vaccination coverage, highlighting a population less engaged with conventional clinic-based prevention.", "limitations": "Small suburban Sydney sample; convenience recruitment and cross-sectional design limit generalisability.", "cidm_contribution": "David A Lewis contribution to outreach-based sexual-health surveillance and service design.", "contradictions_unknowns": "Whether onsite testing programs sustainably improve vaccination/testing uptake requires longitudinal follow-up.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34011431/" }, { "review_event_id": "IRD-20261003-B04-17", "object_id": "CIDM-WORK-1851", "pmid": "33315752", "year": 2021, "title": "Potential and demonstrated impacts of the COVID-19 pandemic on sexually transmissible infections", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Narrative review", "research_question": "How did COVID-19 restrictions and service disruptions alter STI transmission, diagnosis and care?", "methods_summary": "Narrative review of emerging pandemic-era data on sexual behaviour, clinic access, testing and STI surveillance.", "main_finding": "COVID-19 changed sexual networks and reduced access to testing/services; observed STI trends were therefore a mixture of true transmission changes and surveillance/service artefacts.", "limitations": "Early-pandemic review with heterogeneous and rapidly changing evidence; many effects were jurisdiction-specific.", "cidm_contribution": "David A Lewis and Western Sydney sexual-health contribution to interpreting pandemic effects on STI control.", "contradictions_unknowns": "Separating behavioural change from testing under-ascertainment requires longer post-pandemic time series.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/33315752/" }, { "review_event_id": "IRD-20261003-B04-18", "object_id": "CIDM-WORK-1852", "pmid": "33411395", "year": 2021, "title": "Expansion of dysfunctional CD56-CD16+ NK cells in chronic hepatitis B patients", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Human immunology / mechanistic study", "research_question": "Are dysfunctional CD56-CD16+ NK cells expanded in chronic hepatitis B and linked to viral burden?", "methods_summary": "Phenotype and function of NK-cell subsets from 28 chronic-HBV patients were measured by flow cytometry, qPCR, stimulation and dendritic-cell co-culture.", "main_finding": "CD56- NK cells were expanded, expressed more inhibitory and fewer activating receptors, were functionally impaired and correlated positively with serum HBV DNA.", "limitations": "Small mechanistic cohort; association with viral load does not establish whether dysfunctional NK cells are cause or consequence of persistent HBV.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; mechanistic HBV immunology relevant to cure strategies.", "contradictions_unknowns": "Whether restoring this NK-cell compartment improves antiviral control remains untested.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/33411395/" }, { "review_event_id": "IRD-20261003-B04-19", "object_id": "CIDM-WORK-1853", "pmid": "34194408", "year": 2021, "title": "Viral Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma Occurrence and Recurrence", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Review of viral biomarkers", "research_question": "Which HBV-derived biomarkers may improve prediction or detection of HCC occurrence and recurrence beyond conventional surveillance?", "methods_summary": "Review of circulating HBV DNA, RNA transcripts, viral proteins and related viral-host markers relevant to HBV-associated HCC.", "main_finding": "Virus-derived biomarkers may complement host markers and imaging because HBV-host interactions are central to carcinogenesis, but candidate markers vary in validation maturity.", "limitations": "Review evidence; many proposed biomarkers lack large prospective external validation or standardized clinical thresholds.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; integrates HBV virology with cancer-risk stratification.", "contradictions_unknowns": "Which biomarker combinations materially improve clinical outcomes over AFP/ultrasound remains unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34194408/" }, { "review_event_id": "IRD-20261003-B04-20", "object_id": "CIDM-WORK-1854", "pmid": "34217426", "year": 2021, "title": "Long-term protection from HIV infection with oral HIV pre-exposure prophylaxis in gay and bisexual men: findings from the expanded and extended EPIC-NSW prospective implementation study", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Prospective PrEP implementation study", "research_question": "Can low HIV incidence be sustained over several years when high-risk gay and bisexual men receive oral PrEP in routine NSW services?", "methods_summary": "Pragmatic prospective single-arm EPIC-NSW implementation study across 31 sites; 9596 people were dispensed PrEP and followed with HIV/STI testing and dispensing data.", "main_finding": "Over 18,628 person-years there were 30 seroconversions, incidence 1.61/1000 person-years. HIV incidence remained low for up to three years, including transition from study-supplied to subsidised PrEP.", "limitations": "Single-arm implementation study; adherence estimated mainly from medication possession; results depend on affordable access and associated health services.", "cidm_contribution": "David A Lewis / Western Sydney participation in a major NSW HIV-prevention implementation study.", "contradictions_unknowns": "Residual infections clustered with lower adherence and other risk factors; sustaining access and adherence remains central.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34217426/" }, { "review_event_id": "IRD-20261003-B05-01", "object_id": "CIDM-WORK-1855", "pmid": "34161706", "year": 2021, "title": "Azithromycin or Doxycycline for Asymptomatic Rectal Chlamydia trachomatis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Randomized double-blind clinical trial", "research_question": "Is 7-day doxycycline superior to single-dose azithromycin for asymptomatic rectal chlamydia in MSM?", "methods_summary": "Five Australian sexual-health clinics randomized 625 MSM with asymptomatic rectal chlamydia to doxycycline 100 mg twice daily for 7 days or azithromycin 1 g once; microbiologic cure at 4 weeks was the primary endpoint.", "main_finding": "Microbiologic cure was 96.9% with doxycycline versus 76.4% with azithromycin; doxycycline was clearly superior and had fewer gastrointestinal adverse events.", "limitations": "Trial focused on asymptomatic rectal infection in MSM; adherence to a 7-day regimen remains a real-world implementation issue.", "cidm_contribution": "David A Lewis participated in a practice-changing Australian STI treatment trial.", "contradictions_unknowns": "Generalisability to other populations/sites and the balance between efficacy and adherence remain implementation questions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34161706/" }, { "review_event_id": "IRD-20261003-B05-02", "object_id": "CIDM-WORK-1856", "pmid": "35056462", "year": 2021, "title": "Recent Advances in Cryptococcus and Cryptococcosis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Narrative review / special-issue synthesis", "research_question": "What recent advances have changed understanding of Cryptococcus biology, epidemiology, diagnostics and disease?", "methods_summary": "Narrative synthesis of current work across the C. neoformans and C. gattii species complexes.", "main_finding": "The review integrates advances in taxonomy, host-pathogen biology, environmental ecology, molecular epidemiology, diagnostics and treatment challenges.", "limitations": "Narrative overview rather than systematic evidence synthesis; rapidly evolving field.", "cidm_contribution": "Direct CIDM Molecular Mycology authorship through Wieland Meyer.", "contradictions_unknowns": "Major unresolved issues include environmental reservoirs, strain-specific virulence and translation of molecular advances into improved clinical outcomes.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/35056462/" }, { "review_event_id": "IRD-20261003-B05-03", "object_id": "CIDM-WORK-1857", "pmid": "35069461", "year": 2022, "title": "Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Review of diagnostic sequencing technologies", "research_question": "What advantages and limitations do long-read metagenomic technologies offer for clinical diagnosis of fungal infections?", "methods_summary": "Open-access review of long-read sequencing platforms, clinical metagenomics and fungal diagnostic applications.", "main_finding": "Long reads can span diagnostic regions or small genomes and potentially provide species identification, resistance and epidemiological information in one run, but accuracy, cost, workflow standardization and validation remain barriers.", "limitations": "Review of a still-developing technology; clinical performance is heterogeneous and not yet equivalent to validated routine diagnostics.", "cidm_contribution": "Direct CIDM Molecular Mycology contribution through Meyer/Irinyi/Hoang.", "contradictions_unknowns": "How to standardize extraction, databases, analysis and clinical interpretation before routine adoption remains unresolved.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8770865/" }, { "review_event_id": "IRD-20261003-B05-04", "object_id": "CIDM-WORK-1858", "pmid": "34494077", "year": 2021, "title": "Bondi and beyond. Lessons from three waves of COVID-19 from 2020", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Public-health outbreak response narrative", "research_question": "What operational lessons emerged from the first three NSW COVID-19 waves in 2020?", "methods_summary": "Narrative public-health analysis integrating epidemiological linkage and genomic testing across outbreak waves.", "main_finding": "Early waves exposed limits in testing and contact tracing; later response benefited from stronger genomic epidemiology and public-health coordination.", "limitations": "Operational narrative rather than controlled comparative evaluation; multiple interventions changed simultaneously.", "cidm_contribution": "Rebecca Rockett and CIDMLS/CIDM-PH contributed genomic and outbreak-response expertise.", "contradictions_unknowns": "The independent contribution of individual measures cannot be cleanly separated.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34494077/" }, { "review_event_id": "IRD-20261003-B05-05", "object_id": "CIDM-WORK-1859", "pmid": "", "year": 2021, "title": "Mosquitoes associated with an urban estuary and implications for the management of pest and public health risks in Sydney, Australia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Urban estuarine mosquito ecology", "research_question": "Which mosquito species and habitats drive pest and public-health risk in the highly urbanised Cooks River/Wolli Creek estuary?", "methods_summary": "Field mosquito surveillance across urban estuarine habitats was used to characterize species assemblages and management implications.", "main_finding": "The study identified habitat-specific mosquito risks in an urban estuary and emphasized targeted, habitat-aware local management rather than generic mosquito control.", "limitations": "Local ecological study; abundance and public-health risk vary by season and climate, limiting direct transfer to other estuaries.", "cidm_contribution": "Cameron Webb medical-entomology contribution to Sydney vector-risk management.", "contradictions_unknowns": "Long-term effects of habitat restoration, sea-level change and climate variability on mosquito risk need continued surveillance.", "confidence": "MEDIUM", "source_url": "https://doi.org/10.1007/s11273-021-09820-w" }, { "review_event_id": "IRD-20261003-B05-06", "object_id": "CIDM-WORK-1860", "pmid": "34184044", "year": 2021, "title": "Response of Mosquitoes Associated with Estuarine Wetlands to Bushfire in Australia", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Natural-experiment field observation", "research_question": "How do estuarine-wetland mosquitoes respond immediately after bushfire?", "methods_summary": "Existing mosquito-management surveillance captured immature and adult populations after 2019–20 bushfire burned Georges River wetlands.", "main_finding": "Mosquito eggs survived fire impacts and immature stages successfully developed following tidal inundation, indicating rapid persistence/recovery of pest and vector species after bushfire.", "limitations": "Single fire event and habitat system; observational natural experiment without an unburned matched control.", "cidm_contribution": "Cameron Webb medical-entomology surveillance contribution.", "contradictions_unknowns": "Longer-term ecological effects of repeated fires on mosquito community structure remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/34184044/" }, { "review_event_id": "IRD-20261003-B05-07", "object_id": "CIDM-WORK-1861", "pmid": "33671150", "year": 2021, "title": "Assessing the Risk of Exotic Mosquito Incursion through an International Seaport, Newcastle, NSW, Australia", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Urban incursion-risk field survey", "research_question": "How much suitable container habitat exists for exotic Aedes establishment around the Port of Newcastle?", "methods_summary": "More than 300 residential properties adjacent to the port were surveyed; >1500 water-holding containers were recorded.", "main_finding": "Residential environments provide abundant potential breeding habitat, and property appearance was not useful enough to prioritize surveys, implying resource-intensive surveillance/eradication would be required after an incursion.", "limitations": "Habitat suitability is not equivalent to establishment probability; exotic Aedes were not actually detected.", "cidm_contribution": "Cameron Webb/NSW Health Pathology medical-entomology risk assessment.", "contradictions_unknowns": "Actual incursion probability and effectiveness of different response strategies require operational data.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8005993/" }, { "review_event_id": "IRD-20261003-B05-08", "object_id": "CIDM-WORK-1862", "pmid": "33985588", "year": 2021, "title": "Enabling culturally safe sexual health services in western Sydney: a protocol to improve STI treatment outcomes for Aboriginal young people", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Qualitative study protocol", "research_question": "What barriers and enablers shape young Aboriginal people's access to government sexual-health services in Western Sydney?", "methods_summary": "Protocol for purposive recruitment of young health consumers, Aboriginal elders and sexual-health clinicians using culturally informed semi-structured interviews and thematic analysis.", "main_finding": "This is a protocol, not an outcomes paper; it establishes a community-engaged design to generate evidence for service redesign and cultural safety.", "limitations": "No outcome findings should be inferred from the protocol; success depends on recruitment, trust and genuine community partnership.", "cidm_contribution": "David A Lewis/Western Sydney Sexual Health contribution to culturally safe STI-service redesign.", "contradictions_unknowns": "Actual barriers and intervention priorities require linkage to subsequent outcome papers.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8117628/" }, { "review_event_id": "IRD-20261003-B05-09", "object_id": "CIDM-WORK-1863", "pmid": "33431534", "year": 2021, "title": "HSV-associated proctitis presenting without perianal lesions: why testing and empirical treatment may be important", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Clinical case report", "research_question": "Can HSV-2 cause sexually transmitted proctitis without visible perianal or anorectal ulceration?", "methods_summary": "Detailed case report of a man with rectal pain, discharge and bleeding initially treated empirically for gonorrhoea/chlamydia.", "main_finding": "Rectal testing identified HSV-2 after failure of initial antibacterial therapy; valaciclovir led to successful treatment, demonstrating that absent external ulcers do not exclude HSV proctitis.", "limitations": "Single case cannot estimate prevalence or define universal testing thresholds.", "cidm_contribution": "Western Sydney sexual-health clinical diagnostic contribution.", "contradictions_unknowns": "Optimal empirical antiviral criteria in syndromic proctitis require larger diagnostic studies.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7802666/" }, { "review_event_id": "IRD-20261003-B05-10", "object_id": "CIDM-WORK-1864", "pmid": "35457470", "year": 2022, "title": "A Possible Link between the Environment and Cryptococcus gattii Nasal Colonisation in Koalas (Phascolarctos cinereus) in the Liverpool Plains, New South Wales", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "One Health environmental molecular epidemiology", "research_question": "Can C. gattii genotypes in koala nasal colonisation be linked to nearby Eucalyptus tree hollows?", "methods_summary": "169 free-ranging koalas were sampled and geolocated; tree hollows in home ranges were cultured and isolates typed by MLST.", "main_finding": "Nine koalas were culture-positive; colonising genotypes were most consistent with abundant local environmental genotypes, and larger tree hollows were more likely to contain C. gattii.", "limitations": "Association and phylogenetic similarity support but do not prove a specific transmission event from tree to individual koala.", "cidm_contribution": "Direct CIDM Molecular Mycology contribution through Wieland Meyer.", "contradictions_unknowns": "Why only some exposed koalas become colonised or diseased remains unresolved.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9028200/" }, { "review_event_id": "IRD-20261003-B05-11", "object_id": "CIDM-WORK-1865", "pmid": "35491231", "year": 2022, "title": "Finding a Needle in a Haystack - In Silico Search for Environmental Traces of Candida auris", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "In-silico environmental metabarcoding search", "research_question": "Can public sequence repositories reveal environmental traces of Candida auris outside healthcare settings?", "methods_summary": "A subset of NCBI Sequence Read Archive metabarcoding studies was screened using ITS1/ITS2 fungal barcode sequences.", "main_finding": "Thirty-four partial C. auris ITS matches were identified across seven studies, supporting the possibility of a wider environmental distribution.", "limitations": "Short metabarcoding matches can be vulnerable to misclassification and contamination; sequence evidence alone is not culture confirmation of viable environmental C. auris.", "cidm_contribution": "Direct CIDM Molecular Mycology bioinformatics contribution.", "contradictions_unknowns": "Environmental niche, viability and epidemiological relevance of these sequence traces remain uncertain.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/35491231/" }, { "review_event_id": "IRD-20261003-B05-12", "object_id": "CIDM-WORK-1866", "pmid": "35404122", "year": 2022, "title": "Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Benchmarking study / fungal metagenomics", "research_question": "Which sequencing and classification strategies most accurately recover species composition from complex fungal communities?", "methods_summary": "Mock communities containing 43 fungal species were analysed using long- and short-read shotgun/amplicon approaches and multiple taxonomic-classification pipelines.", "main_finding": "Best species-level accuracy came from alignment against fungal-specific databases; query-coverage cutoffs improved classification and abundance estimates with limited data loss.", "limitations": "Mock communities are more controlled than clinical/environmental samples; database completeness remains a major determinant of accuracy.", "cidm_contribution": "Direct CIDM Molecular Mycology and fungal bioinformatics contribution.", "contradictions_unknowns": "Performance in low-biomass, host-rich and previously uncharacterised clinical communities needs continued validation.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9040722/" }, { "review_event_id": "IRD-20261003-B05-13", "object_id": "CIDM-WORK-1867", "pmid": "35333101", "year": 2022, "title": "Barriers and enablers for young Aboriginal people in accessing public sexual health services: A mixed method systematic review", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mixed-method systematic review", "research_question": "What barriers and facilitators influence young Aboriginal people's access to public sexual-health services?", "methods_summary": "Multiple databases and grey literature were searched; 15 studies were included after screening.", "main_finding": "Key facilitators included culturally competent care, integrated testing and self-testing; major barriers included location, inconsistent services, shame and limited STI knowledge.", "limitations": "Heterogeneous studies and service settings; evidence base remains limited and may not fully represent urban Western Sydney.", "cidm_contribution": "David A Lewis contribution to Indigenous sexual-health service evidence.", "contradictions_unknowns": "Which service redesign components produce measurable increases in testing and treatment requires intervention studies.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/35333101/" }, { "review_event_id": "IRD-20261003-B05-14", "object_id": "CIDM-WORK-1868", "pmid": "35918908", "year": 2022, "title": "Engaging hard-to-reach men-who-have-sex-with-men with sexual health screening: Qualitative interviews in an Australian sex-on-premises-venue and sexual health service", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Qualitative interview study", "research_question": "Why do some MSM remain disengaged from routine HIV/STI screening and what service models might reach them?", "methods_summary": "Semi-structured interviews with men using screening services at a sex-on-premises venue and Western Sydney Sexual Health Service; thematic analysis was performed.", "main_finding": "Low perceived risk, privacy concerns, fear and reluctance to disclose behaviour impeded testing; convenience, confidentiality, trust and diverse testing options were valued.", "limitations": "Qualitative convenience sample; views may not generalize to all disengaged MSM.", "cidm_contribution": "David A Lewis/Western Sydney Sexual Health contribution to outreach service design.", "contradictions_unknowns": "Which combination of venue-based, self-testing and clinic services produces sustained engagement needs implementation testing.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9804729/" }, { "review_event_id": "IRD-20261003-B05-15", "object_id": "CIDM-WORK-1869", "pmid": "35627874", "year": 2022, "title": "Citizen Science Mosquito Surveillance by Ad Hoc Observation Using the iNaturalist Platform", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Citizen-science surveillance evaluation", "research_question": "Can ad hoc iNaturalist observations provide useful complementary mosquito surveillance data?", "methods_summary": "Mozzie Monitors iNaturalist records from Oct 2018 to Jul 2021 were analysed for participation, taxonomy, geography and public-health utility.", "main_finding": "The project accumulated 2118 observations covering 57 mosquito species across Australia, demonstrating useful geographic/species information beyond conventional surveillance.", "limitations": "Citizen observations are opportunistic, geographically biased and influenced by participant behaviour and image identifiability.", "cidm_contribution": "Cameron Webb medical-entomology contribution to scalable community surveillance.", "contradictions_unknowns": "How best to calibrate citizen-science observations against systematic trap-based abundance remains open.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9140400/" }, { "review_event_id": "IRD-20261003-B05-16", "object_id": "CIDM-WORK-1870", "pmid": "36354964", "year": 2022, "title": "Japanese Encephalitis Virus Emergence in Australia: Public Health Importance and Implications for Future Surveillance", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Review / public-health perspective", "research_question": "What drove the unprecedented 2022 JEV emergence in Australia and how should surveillance adapt?", "methods_summary": "Review of outbreak activity, plausible virus movement routes, ecological drivers and surveillance needs.", "main_finding": "The 2022 event demonstrated established local transmission involving indigenous mosquitoes, pigs and humans and highlighted the need for integrated animal, vector and human surveillance.", "limitations": "Review written during an evolving outbreak; movement routes and ecological drivers were partly inferential.", "cidm_contribution": "Cameron Webb medical-entomology contribution to national JEV surveillance strategy.", "contradictions_unknowns": "Persistence, overwintering and future geographic spread remain key unresolved surveillance questions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/36354964/" }, { "review_event_id": "IRD-20261003-B05-17", "object_id": "CIDM-WORK-1871", "pmid": "37363260", "year": 2023, "title": "An evaluation of the landscape structure and La Niña climatic anomalies associated with Japanese encephalitis virus outbreaks reported in Australian piggeries in 2022", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Landscape epidemiology / One Health spatial analysis", "research_question": "Which landscape and climate features were associated with 2022 Australian piggery JEV outbreaks?", "methods_summary": "Spatial analysis evaluated ardeid habitat, hydrography, wetlands, land cover and La Niña-associated climate anomalies around reported piggery outbreaks.", "main_finding": "Outbreaks were associated with waterway proximity, temporary wetlands, hydrological flow, ardeid habitat and agricultural landscape structure; landscape features appeared more informative than simple La Niña anomalies alone.", "limitations": "Ecological observational analysis; reported piggery outbreaks are an incomplete proxy for all JEV transmission and sensitive pig-location data constrain replication.", "cidm_contribution": "Cameron Webb/NSW Health Pathology medical-entomology contribution to One Health JEV risk mapping.", "contradictions_unknowns": "Prospective validation is needed before using these features for operational outbreak prediction.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10285696/" }, { "review_event_id": "IRD-20261003-B05-18", "object_id": "CIDM-WORK-1872", "pmid": "37277965", "year": 2023, "title": "Clinicians' perspectives on why young Aboriginal people are not testing for sexually transmissible infections in Western Sydney", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Qualitative clinician interview study", "research_question": "What barriers do clinicians perceive as limiting STI testing among young Aboriginal people in Western Sydney?", "methods_summary": "Sexual-health clinicians and social workers were interviewed; transcripts underwent thematic analysis.", "main_finding": "Personal, practical and programmatic barriers emerged; participants emphasized privacy, community involvement, culturally competent education and co-designed services.", "limitations": "Small clinician-perspective study and does not substitute for direct voices of young Aboriginal people.", "cidm_contribution": "David A Lewis/Western Sydney sexual-health service redesign contribution.", "contradictions_unknowns": "Clinician perceptions must be triangulated with community and consumer perspectives before redesign decisions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37277965/" }, { "review_event_id": "IRD-20261003-B05-19", "object_id": "CIDM-WORK-1873", "pmid": "37336225", "year": 2023, "title": "Antimicrobial susceptibility assays for Neisseria gonorrhoeae: a proof-of-principle population-based retrospective analysis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Population-based retrospective AMR modelling study", "research_question": "Could rapid molecular susceptibility assays reduce ceftriaxone use while preserving appropriate gonorrhoea treatment?", "methods_summary": "23,089 NSW gonococcal isolates from 2008–2019 with susceptibility to ceftriaxone, azithromycin, ciprofloxacin and penicillin were analysed under hypothetical assay-guided treatment strategies.", "main_finding": "Susceptibility patterns varied over time, and isolates with reduced ceftriaxone susceptibility were frequently resistant to other drugs. The analysis supports the potential of multi-drug susceptibility-guided therapy but shows that assay choice must account for correlated resistance.", "limitations": "Retrospective and hypothetical treatment modelling; assumes molecular assays accurately predict phenotype and does not directly test clinical outcomes.", "cidm_contribution": "David A Lewis contribution to gonococcal precision treatment and antimicrobial stewardship.", "contradictions_unknowns": "Real-world assay cost, turnaround, genotype-phenotype accuracy and resistance evolution require prospective implementation studies.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37336225/" }, { "review_event_id": "IRD-20261003-B05-20", "object_id": "CIDM-WORK-1874", "pmid": "37751016", "year": 2023, "title": "Efficacy and Safety of Gepotidacin as Treatment of Uncomplicated Urogenital Gonorrhea (EAGLE-1): Design of a Randomized, Comparator-Controlled, Phase 3 Study", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Phase 3 randomized trial protocol/design", "research_question": "Can oral gepotidacin provide a noninferior alternative to ceftriaxone plus azithromycin for uncomplicated urogenital gonorrhoea?", "methods_summary": "Six-country randomized sponsor-blinded noninferiority phase-3 design; microbiological efficacy population ~400 and safety population ~600, comparing two oral 3000-mg gepotidacin doses with ceftriaxone 500 mg plus azithromycin 1 g.", "main_finding": "This paper reports study design, not efficacy results. Its key contribution is a regulatory-aligned phase-3 framework for testing an oral agent active against many resistant gonococci.", "limitations": "No treatment outcome can be inferred from this protocol/design paper; sponsor involvement and resistance evolution require attention when interpreting later results.", "cidm_contribution": "David A Lewis contributed clinical STI expertise to an important gonorrhoea AMR trial.", "contradictions_unknowns": "Efficacy, safety, site-specific performance and resistance emergence must be judged from the subsequent EAGLE-1 outcome publication.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10581980/" }, { "review_event_id": "IRD-20261003-B06-01", "object_id": "CIDM-WORK-1875", "pmid": "36827395", "year": 2023, "title": "Renal impairment associated with tenofovir disoproxil fumarate for antiretroviral therapy and HIV pre-exposure prophylaxis: An observational cohort study", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Large observational cohort", "research_question": "How common is clinically significant renal impairment among people receiving TDF for PrEP compared with people living with HIV receiving TDF-containing ART?", "methods_summary": "Australian ACCESS data from 52 sexual-health clinics (2009–2019); 5,973 PrEP users and 1,973 people living with HIV were followed for eGFR decline below 60 ml/min/1.73m², with multivariable and propensity-score analyses.", "main_finding": "Renal impairment was uncommon in PrEP users (39/5,973; 0.7%) and more frequent in people living with HIV (81/1,973; 4.1%); the PrEP cohort had substantially lower risk.", "limitations": "Observational design; residual confounding and differences between HIV and PrEP populations remain possible; results focus on marked eGFR decline rather than all renal toxicity.", "cidm_contribution": "David A Lewis/Western Sydney sexual-health participation in a large Australian real-world HIV/PrEP safety cohort.", "contradictions_unknowns": "Optimal renal monitoring intensity for low-risk PrEP users and long-term risk beyond the study period remain implementation questions.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9955644/" }, { "review_event_id": "IRD-20261003-B06-02", "object_id": "CIDM-WORK-1876", "pmid": "36328267", "year": 2023, "title": "An efficient and biodegradable alginate-gelatin hydrogel beads as bait against Aedes aegypti and Aedes albopictus", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mosquito-control materials/feeding experiment", "research_question": "Can biodegradable alginate-gelatin hydrogel beads provide a durable carrier for toxic sugar bait against Aedes mosquitoes?", "methods_summary": "Hydrogel composition and cross-linking were optimized; bait loading was characterized and mosquito mortality after feeding was evaluated, including outdoor applicability.", "main_finding": "The optimized hydrogel bait produced 100% mortality within 72 hours after consumption in tested Aedes aegypti and Aedes albopictus and showed potential for outdoor application.", "limitations": "Mortality after bait consumption does not establish population-level control; field durability, attraction, non-target effects and resistance need larger operational trials.", "cidm_contribution": "Cameron Webb medical-entomology contribution to alternative vector-control technology.", "contradictions_unknowns": "Real-world effectiveness compared with existing attractive toxic sugar bait systems remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/36328267/" }, { "review_event_id": "IRD-20261003-B06-03", "object_id": "CIDM-WORK-1877", "pmid": "16208020", "year": 2005, "title": "Development of a nested qualitative real-time PCR assay to detect Aspergillus species DNA in clinical specimens", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic molecular method evaluation", "research_question": "Can a nested Aspergillus PCR be converted to real-time format to improve turnaround without sacrificing sensitivity?", "methods_summary": "A nested qualitative real-time PCR was implemented on a LightCycler and evaluated on 134 clinical specimens.", "main_finding": "The real-time format significantly shortened reporting time and reduced labour without compromising sensitivity.", "limitations": "Early single-method evaluation; modern Aspergillus diagnostics use more standardized extraction, PCR and biomarker combinations.", "cidm_contribution": "Catriona Halliday, Greg James and Tania Sorrell represent an important Westmead/CIDM fungal molecular-diagnostics lineage.", "contradictions_unknowns": "Contemporary clinical sensitivity/specificity and how the assay compares with modern galactomannan/PCR standards require historical-context interpretation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/16208020/" }, { "review_event_id": "IRD-20261003-B06-04", "object_id": "CIDM-WORK-1878", "pmid": "37686192", "year": 2023, "title": "The Application of 3base™ Technology to Diagnose Eight of the Most Clinically Important Gastrointestinal Protozoan Infections", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Multiplex molecular diagnostic validation", "research_question": "Can an expanded 3base multiplex RT-PCR panel reliably detect eight clinically important gastrointestinal protozoa?", "methods_summary": "EP005 expanded an earlier protozoan panel and was evaluated using 380 clinical samples against commercial or in-house molecular comparators, with cross-reactivity testing against 82 gut organisms.", "main_finding": "All comparator methods showed at least 90% agreement, and EP005 had no cross-reactivity with the tested gut organisms; the assay broadens and streamlines protozoan detection.", "limitations": "Comparator standards differed by target; agreement is not the same as an independent gold-standard sensitivity estimate; real-world cost-effectiveness depends on testing context.", "cidm_contribution": "Westmead Microbiology/CIDMLS contribution to translational multiplex diagnostics.", "contradictions_unknowns": "Prospective clinical impact and performance in low-prevalence settings need further implementation data.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10487386/" }, { "review_event_id": "IRD-20261003-B06-05", "object_id": "CIDM-WORK-1879", "pmid": "24300711", "year": 2014, "title": "Improved detection of gastrointestinal pathogens using generalised sample processing and amplification panels", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Multiplex diagnostic panel evaluation", "research_question": "Can universal sample processing plus multiplex real-time PCR streamline detection of a broad range of gastrointestinal pathogens?", "methods_summary": "487 characterized stool samples plus 81 independent clinical samples were tested with four multiplex real-time PCR panels targeting bacterial, viral, protozoan and C. difficile pathogens.", "main_finding": "Protozoan sensitivity improved and 16 additional mixed infections were detected; C. difficile sensitivity reached 100% against toxigenic culture, while bacterial/viral panels performed comparably to conventional methods with ~3-hour turnaround.", "limitations": "Stored/preselected samples may enrich positives; panel performance depends on comparator quality and target prevalence.", "cidm_contribution": "Direct CIDMLS/ICPMR laboratory contribution to broad multiplex gastrointestinal diagnostics.", "contradictions_unknowns": "Clinical interpretation of additional molecular positives and mixed infections remains important.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/24300711/" }, { "review_event_id": "IRD-20261003-B06-06", "object_id": "CIDM-WORK-1880", "pmid": "25769077", "year": 2015, "title": "Clinical Utility of Urinary Cytology to Detect BK Viral Nephropathy", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Prospective diagnostic test evaluation", "research_question": "How well do urinary decoy cells and urinary SV40T immunocytochemistry screen for BK viral allograft nephropathy compared with viremia and biopsy?", "methods_summary": "704 samples from kidney and kidney-pancreas transplant recipients were compared with histological BKVAN reference diagnosis.", "main_finding": "Quantitative viremia outperformed urine cytology (AUC 0.95 vs 0.79); decoy cells had modest sensitivity and low PPV, while viremia had 96.3% sensitivity and 99.8% NPV.", "limitations": "Low disease prevalence reduces PPV; transplant practice and BK testing algorithms have evolved.", "cidm_contribution": "Direct CIDMLS/ICPMR virology contribution to transplant infection diagnostics.", "contradictions_unknowns": "How best to combine urine and blood markers for current risk-adapted screening remains context dependent.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/25769077/" }, { "review_event_id": "IRD-20261003-B06-07", "object_id": "CIDM-WORK-1881", "pmid": "15508499", "year": 2003, "title": "Tuberculosis in Australia: bacteriologically confirmed cases and drug resistance, 2002: a report of the Australian Mycobacterium Reference Laboratory Network", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "National laboratory surveillance", "research_question": "What was the burden and drug-resistance profile of bacteriologically confirmed tuberculosis in Australia in 2002?", "methods_summary": "Australian Mycobacterium Reference Laboratory Network surveillance summarized culture-confirmed cases and susceptibility results.", "main_finding": "712 laboratory-confirmed TB cases were identified (3.6/100,000); 7.7% of isolates were resistant to at least one first-line drug and 12 isolates (1.9%) were multidrug resistant, predominantly initial rather than acquired resistance.", "limitations": "Laboratory-confirmed surveillance undercounts clinically diagnosed disease and reflects 2002 epidemiology.", "cidm_contribution": "Westmead reference-laboratory participation in national TB surveillance.", "contradictions_unknowns": "Contemporary resistance patterns require current surveillance; historical rates should not be treated as present-day prevalence.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/15508499/" }, { "review_event_id": "IRD-20261003-B06-08", "object_id": "CIDM-WORK-1882", "pmid": "22956746", "year": 2012, "title": "Coxiella burnetii endocarditis after Q fever vaccination", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Case report", "research_question": "Can Q fever endocarditis occur despite prior Q fever vaccination, and what diagnostic lesson follows?", "methods_summary": "Case report of native-valve endocarditis in a vaccinated young man, requiring targeted C. burnetii PCR for definitive diagnosis.", "main_finding": "Prior vaccination did not exclude Q fever endocarditis; culture-negative endocarditis required pathogen-specific molecular testing.", "limitations": "Single case cannot quantify vaccine failure risk or population vaccine effectiveness.", "cidm_contribution": "ICPMR/Westmead diagnostic involvement through Jimmy Ng.", "contradictions_unknowns": "Mechanism of apparent breakthrough infection and the frequency of such events remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/22956746/" }, { "review_event_id": "IRD-20261003-B06-09", "object_id": "CIDM-WORK-1883", "pmid": "38749924", "year": 2024, "title": "Botulism: a mimic for brainstem strokes and Miller Fisher syndrome", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Clinical case report", "research_question": "How can foodborne botulism mimic stroke and Miller Fisher syndrome, and what diagnostic clues can prevent delay?", "methods_summary": "Detailed case report of a 61-year-old man with rapidly progressive cranial neuropathies and descending paralysis after contaminated almond milk exposure.", "main_finding": "Botulism was diagnosed only after later exposure history and toxin testing; antitoxin was delayed until day 16. The case emphasizes descending weakness, cranial involvement and urgent antitoxin when suspected.", "limitations": "Single case; late diagnosis limits inference about treatment effect and diagnostic test sensitivity.", "cidm_contribution": "Westmead laboratory/public-health diagnostic contribution through Jimmy Ng.", "contradictions_unknowns": "Optimal diagnostic pathway when early toxin assays are negative remains a practical challenge.", "confidence": "HIGH", "source_url": "https://www.mja.com.au/journal/2024/220/11/botulism-mimic-brainstem-strokes-and-miller-fisher-syndrome" }, { "review_event_id": "IRD-20261003-B06-10", "object_id": "CIDM-WORK-1884", "pmid": "38408366", "year": 2024, "title": "Inhibition of Cellular Factor TM6SF2 Suppresses Secretion Pathways of Hepatitis B, Hepatitis C, and Hepatitis D Viruses", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic virology / host-factor study", "research_question": "Does the host lipid-trafficking protein TM6SF2 support secretion of HBV, HCV and HDV and therefore represent a shared antiviral target?", "methods_summary": "TM6SF2 knockdown was tested in viral cell-culture models, supplemented by human genetic association data in people with HBV.", "main_finding": "Reduced TM6SF2 lowered secretion of infectious HCV and HDV virions and HBV subviral particles; a human TM6SF2 loss-of-function polymorphism also correlated with lower HBV subviral-particle concentrations.", "limitations": "Host-target inhibition may have metabolic consequences; cell models and genetic associations do not establish therapeutic efficacy or safety.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; cross-virus host-pathway work with pan-viral therapeutic implications.", "contradictions_unknowns": "Therapeutic window and effects on host lipid metabolism require substantial preclinical development.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38408366/" }, { "review_event_id": "IRD-20261003-B06-11", "object_id": "CIDM-WORK-1885", "pmid": "38655824", "year": 2024, "title": "Hepatitis B Virus and Hepatitis C Virus Affect Mitochondrial Function Through Different Metabolic Pathways, Explaining Virus-Specific Clinical Features of Chronic Hepatitis", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Mechanistic cell-metabolism study", "research_question": "Do HBV and HCV perturb mitochondrial metabolism in different ways that could help explain different clinical phenotypes?", "methods_summary": "Seahorse metabolic profiling, membrane-potential assays, pyruvate/lactate measurement, mitochondrial proteomics and isotope-labelled metabolite studies were performed in HBV- and HCV-related cell models.", "main_finding": "Both viruses reduced mitochondrial function and ATP production; HCV impaired glycolysis/fatty-acid oxidation and promoted lipid accumulation, whereas HBV altered pyruvate processing and increased lactate.", "limitations": "Cell-model metabolism does not by itself prove causation of steatosis or carcinogenesis in patients.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; mechanistic link between viral hepatitis and metabolic liver phenotypes.", "contradictions_unknowns": "How these metabolic pathways interact with host genetics, fibrosis and HCC risk in vivo remains unresolved.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11566039/" }, { "review_event_id": "IRD-20261003-B06-12", "object_id": "CIDM-WORK-1886", "pmid": "38742909", "year": 2024, "title": "Arg1 from Cryptococcus neoformans lacks PI3 kinase activity and conveys virulence roles via its IP3-4 kinase activity", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Mechanistic fungal virulence study", "research_question": "Are C. neoformans Arg1 virulence functions driven mainly by IP3-4 kinase activity or by a non-catalytic scaffold role?", "methods_summary": "Kinase-dead and deletion strains, recombinant enzymes, inositol-phosphate profiling, virulence phenotyping and an insect infection model were used.", "main_finding": "Arg1 lacks class-I PI3K activity; its IP3-4 kinase catalytic activity is required for major virulence traits, including thermotolerance, melanization, capsule production and in-vivo virulence.", "limitations": "Insect virulence and fungal-cell phenotypes do not directly establish clinical efficacy of IP3-4K inhibitors.", "cidm_contribution": "Direct CIDM Molecular Mycology mechanistic antifungal-target discovery.", "contradictions_unknowns": "Drugability, fungal selectivity and mammalian safety of this pathway remain to be established.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38742909/" }, { "review_event_id": "IRD-20261003-B06-13", "object_id": "CIDM-WORK-1887", "pmid": "39531642", "year": 2024, "title": "Telehealth Use and Legal Considerations in Drug Health Services During Pandemics: Systematic Scoping Review", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Systematic scoping review", "research_question": "What legal, ethical and clinical issues arise when telehealth is used for drug-health services during pandemics?", "methods_summary": "Six medical and six legal databases plus regulatory standards were searched; 80 publications were included, including legal documents and medical studies.", "main_finding": "Recurring issues were consent/autonomy, confidentiality, privacy, data security and professional indemnity; the literature described frameworks but offered limited evidence on implementation in real drug-health practice.", "limitations": "Scoping review synthesizes heterogeneous legal and medical evidence across jurisdictions; laws and telehealth systems evolve rapidly.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; links infectious-disease/pandemic response with drug-health service governance.", "contradictions_unknowns": "How well legal safeguards are implemented in routine telehealth remains poorly measured.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11599891/" }, { "review_event_id": "IRD-20261003-B06-14", "object_id": "CIDM-WORK-1888", "pmid": "39396554", "year": 2024, "title": "Circulating capsid-antibody-complexes (CACs) drive intrahepatic complement deposition and inform subclinical liver inflammation in chronic hepatitis B", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Translational biomarker/mechanistic study", "research_question": "Do HBV capsid-antibody complexes contribute to complement-mediated liver inflammation and serve as a biomarker of subclinical injury?", "methods_summary": "A serum microplate assay for CACs was developed and applied to untreated chronic-HBV cohorts, with associations to ALT, histology and intrahepatic complement deposition.", "main_finding": "CACs were detected in 77% of untreated patients and associated with ALT, liver inflammation and complement deposition; CACs also identified subclinical inflammation among patients with ALT below 40 IU/ml.", "limitations": "Cross-sectional human associations and mechanistic interpretation require prospective validation; a later corrigendum exists and should remain linked to this record.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; adds humoral/complement immunopathology to HBV disease biology.", "contradictions_unknowns": "Clinical utility thresholds and longitudinal prediction of outcomes need external validation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39396554/" }, { "review_event_id": "IRD-20261003-B06-15", "object_id": "CIDM-WORK-1889", "pmid": "39365832", "year": 2024, "title": "A scoping review of evidence of naturally occurring Japanese encephalitis infection in vertebrate animals other than humans, ardeid birds and pigs", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "PRISMA-guided scoping review", "research_question": "Which vertebrate species beyond people, ardeid birds and pigs show evidence of naturally occurring JEV infection?", "methods_summary": "4,372 records were screened and 62 eligible studies were included; direct and indirect infection evidence was catalogued across vertebrate species.", "main_finding": "Direct JEV evidence was found in multiple mammals and birds, including bats, passerines, cattle, a goat, meerkats and a horse, broadening the potential host landscape beyond canonical bird-pig cycles.", "limitations": "Detection or seropositivity does not establish reservoir or amplifying competence; evidence quality and species identification varied.", "cidm_contribution": "Cameron Webb and Sydney Infectious Diseases Institute contribution to One Health JEV ecology.", "contradictions_unknowns": "Which noncanonical hosts materially contribute to transmission versus acting as dead-end or incidental hosts remains unresolved.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11482687/" }, { "review_event_id": "IRD-20261003-B06-16", "object_id": "CIDM-WORK-1890", "pmid": "39360992", "year": 2024, "title": "Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Bioinformatics pipeline development/benchmark", "research_question": "Can a dedicated pipeline make targeted multi-pathogen enrichment sequencing practical for routine genomic analysis?", "methods_summary": "Castanet was designed for short-read enrichment data with genome reconstruction, contamination discrimination, pathogen-load estimates and QC metrics; benchmark data included multi-strain samples.", "main_finding": "Castanet accurately reconstructed references, handled multiple strains and processed a 96-sample, 50-million-read run in under two hours on a standard computer.", "limitations": "Performance depends on predefined target sets, enrichment design and read quality; prospective clinical validation is separate from computational benchmarking.", "cidm_contribution": "Sydney Infectious Diseases Institute collaboration in scalable pathogen-genomics infrastructure.", "contradictions_unknowns": "Clinical thresholds for low-level positives and contamination require workflow-specific validation.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11494375/" }, { "review_event_id": "IRD-20261003-B06-17", "object_id": "CIDM-WORK-1891", "pmid": "39315958", "year": 2024, "title": "iNaturalist community observations provide valuable data on human-mosquito encounters", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Citizen-science surveillance evaluation", "research_question": "Can iNaturalist observations provide useful passive mosquito surveillance and information on human-mosquito encounters in the UK and Ireland?", "methods_summary": "738 community observations were compared with existing long-term mosquito datasets for distribution, seasonality, species composition and human-biting information.", "main_finding": "Citizen observations broadly reproduced expected seasonal/distribution patterns and added useful information on urban human-mosquito encounters.", "limitations": "Opportunistic submissions are spatially and demographically biased; image-based identification and reporting effort are uneven.", "cidm_contribution": "Cameron Webb contribution to scalable community vector surveillance.", "contradictions_unknowns": "How best to calibrate citizen-science intensity against systematic surveillance remains unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39315958/" }, { "review_event_id": "IRD-20261003-B06-18", "object_id": "CIDM-WORK-1892", "pmid": "39271136", "year": 2024, "title": "Learning outcomes for participants in citizen science mosquito surveillance", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mixed-method citizen-science evaluation", "research_question": "Does participation in mosquito citizen science improve knowledge, skills, self-efficacy and mosquito-control behaviour?", "methods_summary": "Before/after surveys, interviews and assessment of participant mosquito records/photos were used in the Mozzie Monitors program.", "main_finding": "Participants improved mosquito identification and photography skills, reported greater confidence and began more backyard mosquito-management behaviours.", "limitations": "Participants were disproportionately older, female and highly educated; self-selection and before/after design limit causal inference.", "cidm_contribution": "Cameron Webb contribution to public-health education through citizen surveillance.", "contradictions_unknowns": "Durability of learning and whether behaviour change translates into reduced mosquito abundance or disease risk need longer follow-up.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39271136/" }, { "review_event_id": "IRD-20261003-B06-19", "object_id": "CIDM-WORK-1893", "pmid": "39252069", "year": 2024, "title": "Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Sequencing-method benchmark", "research_question": "How do untargeted Illumina, untargeted Oxford Nanopore and targeted viral capture compare for viral diagnostics and surveillance?", "methods_summary": "A six-virus mock community in high host background was tested with untargeted Illumina, ONT and Twist CVRP capture, alongside taxonomic classifiers and host-transcriptome analysis.", "main_finding": "Targeted capture improved sensitivity by at least 10–100-fold and detected low viral loads around 60 genome copies/ml; untargeted ONT was faster and specific at high loads but less sensitive at lower loads without longer sequencing.", "limitations": "Controlled mock samples do not fully represent clinical diversity; targeted capture inherently misses organisms outside the bait set.", "cidm_contribution": "Sydney Infectious Diseases Institute contribution to clinical/pathogen genomics methodology.", "contradictions_unknowns": "No single workflow dominates all contexts; cost, turnaround, discovery potential and sensitivity must be balanced.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11382446/" }, { "review_event_id": "IRD-20261003-B06-20", "object_id": "CIDM-WORK-1894", "pmid": "39127450", "year": 2024, "title": "BCG vaccination of healthcare workers for protection against COVID-19: 12-month outcomes from an international randomised controlled trial", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Phase III double-blind randomized controlled trial", "research_question": "Does BCG-Denmark reduce symptomatic or severe COVID-19 over 12 months in healthcare workers?", "methods_summary": "3,988 healthcare workers were randomized 1:1 to BCG-Denmark or saline across five countries; 3,386 SARS-CoV-2-naïve participants entered the modified intention-to-treat analysis.", "main_finding": "BCG did not protect against COVID-19: symptomatic COVID-19 was slightly more frequent with BCG (22.6% vs 19.6%), while severe COVID-19 was not significantly reduced.", "limitations": "Pandemic conditions and subsequent COVID vaccination changed during follow-up; severe-event definitions included work-absence outcomes and hospitalization numbers were small.", "cidm_contribution": "Mark W Douglas contribution to a large international randomized pandemic trial.", "contradictions_unknowns": "Any heterologous BCG benefit may depend on pathogen, timing or population, but this trial does not support COVID-19 protection in healthcare workers.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11409612/" }, { "review_event_id": "IRD-20261003-B07-01", "object_id": "CIDM-WORK-1895", "pmid": "39074411", "year": 2024, "title": "Characterising the molecular epidemiology of human parechovirus in young infants in the UK and Canada", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular epidemiology / phylogenetic study", "research_question": "How genetically diverse were human parechoviruses infecting young infants in the UK and Canada, and was viral sequence associated with severity, place or time?", "methods_summary": "Next-generation sequencing and VP1-region phylogenetic analysis of infant PeV infections collected during 2013–2018, with comparison to Australian outbreak sequences.", "main_finding": "Most sequences were PeV-A3 and clustered closely, with no significant association between sequence variation and ICU-level severity, geography or sampling year in this small cohort.", "limitations": "Only 58 samples were sequenced; limited statistical power and VP1-focused phylogeny may miss variation elsewhere in the genome.", "cidm_contribution": "Tanya Golubchik/Sydney Infectious Diseases Institute contribution to cross-country viral genomic epidemiology.", "contradictions_unknowns": "Larger, more recent datasets are needed to test whether lineage changes contribute to severe infant disease.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39074411/" }, { "review_event_id": "IRD-20261003-B07-02", "object_id": "CIDM-WORK-1896", "pmid": "39044997", "year": 2024, "title": "Developing and validating a scale to measure the perceptions of safety, usability and acceptability of microarray patches for vaccination: a study protocol", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Scale-development study protocol", "research_question": "How can perceptions of safety, usability and acceptability of vaccine microarray patches be measured reliably across target groups?", "methods_summary": "Three-phase scale-development protocol using interviews, literature-derived items, expert/target-population review and formal psychometric evaluation.", "main_finding": "This is a protocol, not an outcome paper; it defines a structured process for developing and validating a MAP acceptability instrument.", "limitations": "No validated scale or behavioural outcome is reported in this paper.", "cidm_contribution": "Sydney Infectious Diseases Institute/Western Sydney public-health contribution to vaccine-delivery implementation research.", "contradictions_unknowns": "Predictive validity for real-world vaccine uptake will require subsequent validation studies.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39044997/" }, { "review_event_id": "IRD-20261003-B07-03", "object_id": "CIDM-WORK-1897", "pmid": "38953434", "year": 2024, "title": "Reconstruction of the historic time course of blood-borne virus contamination of clotting factor concentrates, 1974-1992", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Historical molecular virology / product surveillance", "research_question": "Which blood-borne viruses contaminated historical clotting-factor concentrates and how did contamination change with manufacturing practices?", "methods_summary": "Twenty-four preserved factor VIII/IX concentrates dated 1974–1992 were tested by quantitative molecular assays for multiple blood-borne viruses.", "main_finding": "HCV and HPgV-1 were most frequently detected, often at high loads before mid-1980s virus-inactivation changes; B19V and PARV4 persisted later, illustrating differential resistance to manufacturing controls.", "limitations": "Small surviving product archive and potential storage degradation; detection in products does not directly quantify recipient infection risk.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to historical viral genomics and blood-safety reconstruction.", "contradictions_unknowns": "The exact relation between archived product contamination and individual patient exposure remains incompletely reconstructable.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38953434/" }, { "review_event_id": "IRD-20261003-B07-04", "object_id": "CIDM-WORK-1898", "pmid": "38935906", "year": 2024, "title": "Candida albicans-A systematic review to inform the World Health Organization Fungal Priority Pathogens List", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Systematic review for WHO priority-setting", "research_question": "What is the global burden, mortality, resistance and preventability of invasive Candida albicans infection?", "methods_summary": "Systematic search of PubMed and Web of Science for 2016–2021 evidence on incidence, mortality, morbidity, resistance, preventability and emergence.", "main_finding": "C. albicans remained the most common invasive Candida species with high mortality; resistance was generally uncommon but some azole-resistance increases were reported, while data from low-income settings and on sequelae were sparse.", "limitations": "Heterogeneous international evidence and substantial data gaps; a later erratum is linked to the paper.", "cidm_contribution": "Tania Sorrell/Sydney ID and Westmead fungal expertise contributed directly to WHO fungal-priority evidence.", "contradictions_unknowns": "Attributable mortality, long-term morbidity and resistance trends in underrepresented regions need better prospective data.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38935906/" }, { "review_event_id": "IRD-20261003-B07-05", "object_id": "CIDM-WORK-1899", "pmid": "38914564", "year": 2024, "title": "Improving the representativeness of UK's national COVID-19 Infection Survey through spatio-temporal regression and post-stratification", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Statistical survey-methodology study", "research_question": "Can spatio-temporal regression and post-stratification correct participation-related bias in national SARS-CoV-2 infection surveys?", "methods_summary": "Models were applied to over 6.4 million PCR tests and 1.9 million antibody tests from the UK COVID-19 Infection Survey across age, region, ethnicity and vaccination strata.", "main_finding": "Post-stratification modestly changed PCR-positivity estimates but materially corrected antibody estimates, with errors up to 21 percentage points when vaccination status was ignored.", "limitations": "Model validity depends on covariate measurement and assumptions about participation mechanisms; results are survey-system specific.", "cidm_contribution": "Tanya Golubchik-linked population genomics/surveillance collaboration.", "contradictions_unknowns": "Residual non-response bias and transferability to future pathogens/surveys require further evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38914564/" }, { "review_event_id": "IRD-20261003-B07-06", "object_id": "CIDM-WORK-1900", "pmid": "38813447", "year": 2024, "title": "Cost-effectiveness of diagnosis and treatment of early gestational diabetes mellitus: economic evaluation of the TOBOGM study, an international multicenter randomized controlled trial", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Trial-based economic evaluation", "research_question": "Is diagnosing and treating early GDM before 20 weeks cost-effective compared with usual later screening/treatment?", "methods_summary": "Healthcare-resource use from the TOBOGM RCT was costed; intention-to-treat, multiple imputation and bootstrap cost-effectiveness analysis were used.", "main_finding": "Early diagnosis/treatment reduced composite adverse pregnancy outcomes by about 5.6 percentage points and tended to lower costs by about US$1,373, with high probability of cost-effectiveness.", "limitations": "Short-term healthcare perspective; long-term maternal/child health and economic effects were not captured.", "cidm_contribution": "Western Sydney health-economics collaboration within the broader research network.", "contradictions_unknowns": "Long-term cost-effectiveness and performance under different health-system prices remain open.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38813447/" }, { "review_event_id": "IRD-20261003-B07-07", "object_id": "CIDM-WORK-1901", "pmid": "38774675", "year": 2024, "title": "Bacille Calmette-Guérin vaccination to prevent febrile and respiratory illness in adults (BRACE): secondary outcomes of a randomised controlled phase 3 trial", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Phase 3 randomized controlled trial secondary outcomes", "research_question": "Does BCG reduce febrile or respiratory illness in adult healthcare workers over 12 months?", "methods_summary": "6,828 healthcare workers at 36 centres were randomized to BCG-Denmark or control and followed for prespecified febrile/respiratory outcomes.", "main_finding": "BCG did not reduce severe illness and was associated with a small increase in experiencing at least one febrile/respiratory illness episode; no major safety concerns emerged.", "limitations": "Secondary outcomes; pandemic-period exposures and later COVID vaccination complicate interpretation of heterologous effects.", "cidm_contribution": "Large international BRACE collaboration with Westmead-linked investigators.", "contradictions_unknowns": "Adult heterologous BCG effects may vary by pathogen and context, but this trial does not support broad respiratory protection.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38774675/" }, { "review_event_id": "IRD-20261003-B07-08", "object_id": "CIDM-WORK-1902", "pmid": "38663355", "year": 2024, "title": "Specific and off-target immune responses following COVID-19 vaccination with ChAdOx1-S and BNT162b2 vaccines-an exploratory sub-study of the BRACE trial", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Prospective immunology sub-study", "research_question": "Do ChAdOx1-S and BNT162b2 alter immune responses to unrelated pathogens as well as SARS-CoV-2?", "methods_summary": "Blood from 284 healthcare workers before and after vaccination was tested for SARS-CoV-2 antibodies and cytokine responses to several unrelated microbial stimuli.", "main_finding": "Both vaccines induced strong SARS-CoV-2 responses and measurably altered cytokine responses to unrelated pathogens, with patterns differing between vaccine platforms.", "limitations": "Exploratory immune endpoints do not establish clinical protection or harm from off-target responses.", "cidm_contribution": "BRACE/Sydney infectious-disease immunology collaboration.", "contradictions_unknowns": "Clinical relevance, duration and mechanism of the heterologous cytokine changes remain uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38663355/" }, { "review_event_id": "IRD-20261003-B07-09", "object_id": "CIDM-WORK-1903", "pmid": "38637955", "year": 2024, "title": "Posttraumatic stress disorder (PTSD) and complex PTSD in eating disorder treatment-seekers: Prevalence and associations with symptom severity", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Cross-sectional clinical psychopathology study", "research_question": "How common are ICD-11 PTSD and complex PTSD among eating-disorder treatment seekers, and how are symptoms related to eating-disorder severity?", "methods_summary": "217 treatment-seeking participants across residential, partial-hospital and outpatient services completed trauma and eating-disorder measures.", "main_finding": "Probable CPTSD was much more common than PTSD (28.4% vs 3.8%); disturbances in self-organization were independently associated with greater eating-disorder severity and impairment.", "limitations": "Cross-sectional self-report study in treatment seekers; diagnostic status was probable rather than clinician-confirmed.", "cidm_contribution": "Included via broader verified core-person/institutional lineage; not a CIDM microbiology-specific scientific theme.", "contradictions_unknowns": "Prospective work is needed to test whether trauma-focused treatment improves eating-disorder outcomes.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38637955/" }, { "review_event_id": "IRD-20261003-B07-10", "object_id": "CIDM-WORK-1904", "pmid": "38626958", "year": 2024, "title": "Multicentre double-blind randomised placebo-controlled trial evaluating the efficacy of the meningococcal B vaccine, 4CMenB (Bexsero), against Neisseria gonorrhoeae infection in men who have sex with men: the GoGoVax study protocol", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Randomized controlled trial protocol", "research_question": "Can 4CMenB provide clinically meaningful cross-protection against gonorrhoea in high-risk GBM+ populations?", "methods_summary": "Double-blind placebo-controlled multicentre protocol enrolling high-risk GBM+ participants with prior gonorrhoea/syphilis; outcome is gonococcal infection efficacy.", "main_finding": "This paper reports the trial design only; it does not provide vaccine-efficacy results.", "limitations": "No outcome inference should be made before linked trial results are available.", "cidm_contribution": "David A Lewis contributes Western Sydney sexual-health and gonorrhoea expertise.", "contradictions_unknowns": "True 4CMenB efficacy, site-specific protection and duration must be judged from outcome publications.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38626958/" }, { "review_event_id": "IRD-20261003-B07-11", "object_id": "CIDM-WORK-1905", "pmid": "38493135", "year": 2024, "title": "Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Targeted metagenomic cohort study", "research_question": "Are respiratory co-detections associated with RSV disease severity in infants?", "methods_summary": "Targeted sequencing of >100 pathogens was applied to nasopharyngeal samples from 433 RSV-positive infants across two European cohorts.", "main_finding": "Additional viruses were common but only modestly related to severity; Haemophilus co-detection was strongly associated with worse severity and hospitalization (OR about 4.25).", "limitations": "Co-detection is not proof of causal co-infection; residual confounding and colonization versus pathogenicity remain issues.", "cidm_contribution": "Tanya Golubchik/Sydney ID genomic-surveillance contribution.", "contradictions_unknowns": "Prospective mechanistic studies are required to establish whether Haemophilus contributes causally to severe RSV.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38493135/" }, { "review_event_id": "IRD-20261003-B07-12", "object_id": "CIDM-WORK-1906", "pmid": "38419267", "year": 2024, "title": "Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic blood-safety evaluation", "research_question": "Can confirmatory anti-HBc testing reduce false donor deferral while preserving HBV safety, and how might screening affect rare blood groups?", "methods_summary": "397 HBsAg-negative, initially anti-HBc-reactive donor samples were retested across five assays and donor ethnicity/rare blood-group representation analysed.", "main_finding": "Using two anti-HBc assays improved confirmation of true HBV exposure, but confirmed anti-HBc positivity was enriched among minority-ethnic donors and could disproportionately reduce rare-blood availability.", "limitations": "Single national blood-service context; assay performance and donor demographics may differ elsewhere.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to blood-safety and assay interpretation.", "contradictions_unknowns": "The optimal balance between HBV safety and maintaining rare-donor supply requires service-specific policy modelling.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38419267/" }, { "review_event_id": "IRD-20261003-B07-13", "object_id": "CIDM-WORK-1907", "pmid": "38383783", "year": 2024, "title": "Prevalence of persistent SARS-CoV-2 in a large community surveillance study", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Large community genomic surveillance study", "research_question": "How frequent are persistent SARS-CoV-2 infections and what evolutionary/clinical features do they show?", "methods_summary": "National survey sequence data were used to identify prolonged high-titre infections and analyse viral evolution and self-reported long COVID.", "main_finding": "381 persistent infections lasting at least 30 days were identified, including 54 lasting at least 60 days; estimated 0.1–0.5% of infections may persist, with >50% higher odds of long-COVID reporting.", "limitations": "Persistent RNA does not prove ongoing replication in every case; long-COVID association is observational.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to viral-evolution surveillance.", "contradictions_unknowns": "The fraction of persistent infections that generate transmissible novel lineages remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38383783/" }, { "review_event_id": "IRD-20261003-B07-14", "object_id": "CIDM-WORK-1908", "pmid": "38307854", "year": 2024, "title": "Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Large longitudinal population surveillance analysis", "research_question": "What predicts SARS-CoV-2 reinfection across successive Omicron waves?", "methods_summary": "About 45,000 reinfections from the UK national infection survey were analysed across BA.1, BA.2, BA.4/5 and later waves.", "main_finding": "Reinfections were generally milder and lower viral load than first infections; protection was stronger after more recent variants but waned over time, and recent vaccination reduced reinfection risk.", "limitations": "Observational estimates depend on testing frequency, variant assignment and changing population immunity.", "cidm_contribution": "Large-scale genomic/population analysis linked to Tanya Golubchik/Sydney ID collaboration.", "contradictions_unknowns": "Future variant immune escape may change the balance between prior-infection and vaccine protection.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38307854/" }, { "review_event_id": "IRD-20261003-B07-15", "object_id": "CIDM-WORK-1909", "pmid": "38081203", "year": 2024, "title": "Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular transmission epidemiology", "research_question": "Which demographic groups contributed disproportionately to HIV-1 transmission in PopART communities in Zambia?", "methods_summary": "Deep sequencing from 7,124 participants identified 300 likely transmission pairs, followed by demographic weighting and source-characteristic analysis.", "main_finding": "Men transmitted roughly twice as many infections per capita as women, with men aged 25–40 prominent sources; importation and drug-resistant virus were not dominant drivers.", "limitations": "Phylogenetic linkage infers likely rather than proven transmission pairs; unsampled infections can distort source attribution.", "cidm_contribution": "Tanya Golubchik genomic epidemiology contribution to HIV prevention targeting.", "contradictions_unknowns": "How prevention strategies for underserved men change transmission networks needs prospective evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38081203/" }, { "review_event_id": "IRD-20261003-B07-16", "object_id": "CIDM-WORK-1910", "pmid": "38050831", "year": 2023, "title": "Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Clinical diagnostic validation", "research_question": "Can veSEQ-HIV NGS replace Sanger/ViroSeq for routine HIV drug-resistance testing in an Australian diagnostic laboratory?", "methods_summary": "The probe-based whole-genome NGS assay was benchmarked for resistance-mutation detection, subtype accuracy, reproducibility and small-batch laboratory implementation.", "main_finding": "veSEQ-HIV achieved 100% accuracy for major mutations, 98% for minor mutations and 100% subtype accuracy when >1,000 reads mapped, and successfully replaced ViroSeq in the laboratory.", "limitations": "Performance depends on adequate viral reads and local workflow; broader inter-laboratory reproducibility still matters.", "cidm_contribution": "Australian clinical genomics contribution through Tanya Golubchik and collaborators.", "contradictions_unknowns": "Ongoing validation is needed as ART targets and resistance interpretation evolve.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/38050831/" }, { "review_event_id": "IRD-20261003-B07-17", "object_id": "CIDM-WORK-1911", "pmid": "40475921", "year": 2025, "title": "Listeria monocytogenes Endophthalmitis-Good Outcome With Rapid Diagnosis Using MALDI-TOF and Treatment With Benzylpenicillin and Trimethoprim-Sulfamethoxazole", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Clinical case report", "research_question": "Can rapid microbiological diagnosis and prolonged targeted antibiotic therapy preserve vision in endogenous Listeria endophthalmitis?", "methods_summary": "Case report of a 79-year-old man with gastrointestinal Listeria infection, bacteraemia and endogenous endophthalmitis diagnosed rapidly using MALDI-TOF.", "main_finding": "Three weeks of benzylpenicillin plus six weeks of trimethoprim-sulfamethoxazole achieved a comparatively good visual outcome with only mild-to-moderate residual deficit.", "limitations": "Single case cannot define optimal regimen or treatment duration.", "cidm_contribution": "Direct CIDM affiliation through Mark Douglas and Westmead microbiology.", "contradictions_unknowns": "Comparative effectiveness of dual therapy versus other regimens remains unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/40475921/" }, { "review_event_id": "IRD-20261003-B07-18", "object_id": "CIDM-WORK-1912", "pmid": "39761810", "year": 2025, "title": "Current status of immunisation for herpes zoster", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Narrative vaccine review", "research_question": "What is the current evidence for recombinant zoster vaccination in older and immunocompromised people?", "methods_summary": "Narrative review of zoster burden, recombinant glycoprotein-E/AS01B vaccine efficacy, durability and performance in immunocompromised groups.", "main_finding": "Recombinant zoster vaccine provides >90% efficacy in immunocompetent adults with protection remaining >80% at 11 years, and substantial efficacy/immunogenicity in severely immunocompromised patients.", "limitations": "Narrative synthesis; subgroup evidence varies in size and quality and continues to evolve.", "cidm_contribution": "Direct CIDMLS affiliation through Janette Taylor and Westmead vaccine/virology expertise.", "contradictions_unknowns": "Optimal boosting and protection in specific immunosuppressed subgroups require longer follow-up.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39761810/" }, { "review_event_id": "IRD-20261003-B07-19", "object_id": "CIDM-WORK-1913", "pmid": "40753672", "year": 2025, "title": "Influenza vaccination in patients with heart failure compared to usual practice: A model-based cost-effectiveness analysis", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Model-based health-economic evaluation", "research_question": "Would offering free influenza vaccination before discharge to hospitalized heart-failure patients in China be cost-effective versus usual care?", "methods_summary": "One-year four-state Markov model compared discharge vaccination with usual community-based access, using health-system costs and outcomes including QALYs, readmissions and death.", "main_finding": "The intervention was dominant in the model: about US$443 lower cost and 0.03 higher QALYs per patient, with estimated reductions in influenza-like illness, readmission and death.", "limitations": "Model outputs depend on assumed effectiveness and event rates; not itself randomized clinical-outcome evidence.", "cidm_contribution": "Direct CIDM-PH affiliation through Rong Liu; links vaccination implementation with health economics.", "contradictions_unknowns": "Real-world implementation costs and effect sizes should be tested against trial and service data.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/40753672/" }, { "review_event_id": "IRD-20261003-B07-20", "object_id": "CIDM-WORK-1914", "pmid": "40897187", "year": 2025, "title": "Influenza vaccination to improve outcomes for patients with acute heart failure (PANDA II): a multiregional, seasonal, hospital-based, cluster-randomised, controlled trial in China", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Pragmatic cluster-randomized controlled trial", "research_question": "Does providing free influenza vaccination before discharge improve 12-month outcomes after acute heart-failure hospitalization?", "methods_summary": "164 hospitals and 7,771 participants were included over three influenza seasons; hospitals were cluster-randomized to inpatient vaccination access versus usual care.", "main_finding": "The composite of death or readmission occurred in 41.2% of vaccinated-group participants versus 47.0% with usual care (OR 0.83), with fewer serious adverse events in the vaccination group.", "limitations": "Cluster design and seasonal/hospital implementation can introduce site-level heterogeneity; sponsor involvement and external generalizability should be considered.", "cidm_contribution": "Direct CIDM-PH affiliation through Rong Liu; high-impact implementation trial connecting infectious-disease prevention and cardiovascular outcomes.", "contradictions_unknowns": "Generalisability outside China and the relative contribution of reduced influenza versus broader care-process effects require further study.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/40897187/" }, { "review_event_id": "IRD-20261003-B08-01", "object_id": "CIDM-WORK-1915", "pmid": "41427434", "year": 2025, "title": "Polyfunctional T peripheral helper cells are associated with the magnitude and durability of antibody responses after COVID-19", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Longitudinal human immunology study", "research_question": "Which SARS-CoV-2-specific T-cell features are associated with the magnitude and durability of antibody responses after infection?", "methods_summary": "67 unvaccinated adults with Wuhan-strain infection were followed for up to 14 months; antibody and bulk T-cell responses were measured, with detailed flow-cytometric analysis of spike-specific T-cell subsets in 14 participants.", "main_finding": "Early polyfunctional IL-21-producing peripheral helper T cells correlated strongly with early antibody magnitude and predicted neutralising-antibody maintenance about a year later; antibodies declined but remained detectable in most participants.", "limitations": "Detailed cellular phenotyping was performed in a small subset; observational correlations do not prove that Tph cells cause durable humoral immunity.", "cidm_contribution": "Westmead/CIDMLS-linked COVID-19 immunology through Janette Taylor and collaborators.", "contradictions_unknowns": "Whether Tph signatures can prospectively predict vaccine durability or be therapeutically manipulated remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/41427434/" }, { "review_event_id": "IRD-20261003-B08-02", "object_id": "CIDM-WORK-1916", "pmid": "41320130", "year": 2025, "title": "Hepatitis B viral DNA integration occurs within three days of infection and is enhanced by ATR inhibition", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic HBV integration study", "research_question": "How early after HBV infection does viral DNA integration occur, and which host DNA-repair pathways influence it?", "methods_summary": "A replication-deficient HBV reporter was used in HepG2-NTCP cells; double-strand breaks and inhibitors of DNA-repair pathways were applied at defined timepoints after infection.", "main_finding": "HBV integration occurred within hours to days. X-ray-induced breaks increased integration 2–3-fold; ATR inhibition increased it 2.4–2.8-fold, whereas microhomology-mediated end joining inhibition reduced integration to about 17% of control.", "limitations": "Cell-culture reporter system; the frequency and repair-pathway balance in natural human infection may differ.", "cidm_contribution": "Mark W Douglas/Storr Liver Centre/Sydney ID contribution to HBV oncogenesis mechanisms.", "contradictions_unknowns": "Whether targeting integration pathways can safely reduce HBV-associated HCC risk in vivo is unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/41320130/" }, { "review_event_id": "IRD-20261003-B08-03", "object_id": "CIDM-WORK-1917", "pmid": "39859671", "year": 2025, "title": "Citric Acid and Sodium Bicarbonate as an Alternative Carbon Dioxide Source for Mosquito Surveillance", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Laboratory and field mosquito-surveillance evaluation", "research_question": "Can low-cost citric-acid/sodium-bicarbonate CO2 generation substitute for dry ice in mosquito traps?", "methods_summary": "CO2 production was evaluated in laboratory experiments and acid-baited traps were compared with dry-ice traps at urban and peri-urban Sydney sites.", "main_finding": "The acid system produced overnight CO2 sufficient for trapping. Dry ice captured up to 59% more mosquitoes overall, but catches were similar in the urban setting and species composition was comparable.", "limitations": "Only two field sites and a prototype formulation; lower capture at one site may limit sensitivity for low-density surveillance.", "cidm_contribution": "Cameron Webb medical-entomology contribution to lower-cost field surveillance.", "contradictions_unknowns": "Optimization of CO2 output and validation across climates, trap types and low-abundance populations are still needed.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39859671/" }, { "review_event_id": "IRD-20261003-B08-04", "object_id": "CIDM-WORK-1918", "pmid": "41233774", "year": 2025, "title": "Disseminated Bacillus Calmette-Guerin infection following concurrent intravesical BCG therapy and immune checkpoint inhibitior therapy: a case report", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Clinical case report", "research_question": "Can disseminated BCG infection complicate concurrent intravesical BCG and immune-checkpoint-inhibitor therapy and mimic malignancy?", "methods_summary": "Detailed case report of an 86-year-old man with relapsed Hodgkin lymphoma and bladder cancer receiving checkpoint inhibition and intravesical BCG; diagnosis used PCR and mycobacterial culture.", "main_finding": "The patient developed mycotic aortic aneurysm, psoas abscess and vertebral osteomyelitis caused by M. bovis BCG and died despite antimycobacterial therapy and drainage.", "limitations": "Single case cannot establish that immune checkpoint inhibition caused BCG dissemination.", "cidm_contribution": "Direct CIDM and NSW Mycobacterium Reference Laboratory contribution through Indy Sandaradura and colleagues.", "contradictions_unknowns": "The degree to which checkpoint inhibition alters BCG dissemination risk remains uncertain and needs broader pharmacovigilance.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12616909/" }, { "review_event_id": "IRD-20261003-B08-05", "object_id": "CIDM-WORK-1919", "pmid": "39749570", "year": 2025, "title": "Novel digital droplet inverse PCR assay shows that natural clearance of hepatitis B infection is associated with fewer viral integrations", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Assay-development and human tissue study", "research_question": "Is the burden of integrated HBV DNA lower after natural HBsAg loss, and can it be measured sensitively in clinical tissue?", "methods_summary": "A dd-qinvPCR method was developed and applied to 32 liver resections and 10 fine-needle aspirates from anti-HBc-positive, HBeAg-negative individuals.", "main_finding": "The assay detected integration from fewer than 80 cells. Integrated HBV DNA was about 9-fold lower in HBsAg-negative than HBsAg-positive liver samples.", "limitations": "Small clinical sample and cross-sectional comparison; association does not show whether fewer integrations cause or result from viral clearance.", "cidm_contribution": "Mark W Douglas/Storr Liver Centre contribution to HBV cure biomarkers and integration biology.", "contradictions_unknowns": "Longitudinal changes in integrated HBV DNA and their ability to predict functional cure remain to be tested.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39749570/" }, { "review_event_id": "IRD-20261003-B08-06", "object_id": "CIDM-WORK-1920", "pmid": "39787316", "year": 2025, "title": "Equipping residential aged care facilities for acute respiratory illness: The Western Sydney experience of improving outbreak management", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Naturalistic implementation case study", "research_question": "How did sustained public-health-unit engagement improve respiratory-outbreak preparedness and management in Western Sydney aged-care facilities?", "methods_summary": "Naturalistic case study with critical thematic analysis of Western Sydney Public Health Unit work with residential aged-care facilities during influenza outbreaks from 2014–2019.", "main_finding": "Long-term stakeholder engagement, staff capacity building and research-informed action were associated with timelier public-health response and improved outbreak-management capability.", "limitations": "Uncontrolled implementation case study; improvements cannot be attributed to individual program components with causal certainty.", "cidm_contribution": "Western Sydney public-health/CIDM-PH lineage linking outbreak response with aged-care preparedness.", "contradictions_unknowns": "Which components are most scalable and how gains persist under novel pathogens require prospective evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/39787316/" }, { "review_event_id": "IRD-20261003-B08-07", "object_id": "CIDM-WORK-1921", "pmid": "40976373", "year": 2025, "title": "Phage therapy: An international survey of attitudes and experiences amongst clinicians", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "International clinician survey", "research_question": "What are clinicians' current attitudes, experience and practical barriers regarding phage therapy?", "methods_summary": "An anonymized survey was distributed to >300 members of Global Clinical Phage Rounds from October 2024 to January 2025.", "main_finding": "Thirty clinicians responded (9.6%); 93% would consider enrolment in phage-therapy RCTs. Priorities included Pseudomonas, Klebsiella and S. aureus, while evidence gaps, regulation and phage access were key barriers.", "limitations": "Very low response rate and highly selected expert network; results are not representative of clinicians generally.", "cidm_contribution": "Direct CIDM affiliation through Ruby Lin; translational contribution to phage-therapy implementation.", "contradictions_unknowns": "How attitudes differ in less-experienced settings and whether stronger trial evidence changes uptake remain unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/40976373/" }, { "review_event_id": "IRD-20261003-B08-08", "object_id": "CIDM-WORK-1922", "pmid": "41190822", "year": 2025, "title": "mGem: Immune recognition and clearance of bacteriophages-implications for phage therapy", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Perspective / mechanistic review", "research_question": "How does host immunity limit systemic phage therapy and what design strategies might improve persistence?", "methods_summary": "Perspective synthesizing innate and adaptive immune recognition and clearance of therapeutic bacteriophages.", "main_finding": "The article emphasizes that >99% of circulating phages may be cleared within hours after injection and argues for selection or engineering of immunologically camouflaged second- and third-generation phages.", "limitations": "Perspective rather than new clinical efficacy study; quantitative clearance varies by phage, host and route.", "cidm_contribution": "Westmead/WIMR phage-immunology collaboration.", "contradictions_unknowns": "How to balance immune evasion, safety, bacterial killing and manufacturability remains an open translational problem.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/41190822/" }, { "review_event_id": "IRD-20261003-B08-09", "object_id": "CIDM-WORK-1923", "pmid": "40164150", "year": 2025, "title": "Synthesis of a New Purine Analogue Class with Antifungal Activity and Improved Potency against Fungal IP3-4K", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Medicinal chemistry / antifungal target-validation study", "research_question": "Can pharmacological inhibition of fungal inositol-polyphosphate kinases produce direct antifungal activity and synergy with amphotericin B?", "methods_summary": "Purine analogues were synthesized and tested against recombinant and cellular Arg1/Kcs1, fungal growth and an insect cryptococcosis model.", "main_finding": "DT-23 inhibited Arg1 and Kcs1 at submicromolar concentrations, inhibited C. neoformans growth, synergized with amphotericin B and improved protection in an insect infection model.", "limitations": "Early preclinical work; MIC, pharmacokinetics, mammalian toxicity and selectivity require substantial optimization before clinical translation.", "cidm_contribution": "Direct CIDM Molecular Mycology contribution; first pharmacological validation of this fungal IPK strategy.", "contradictions_unknowns": "Whether IPK inhibition can achieve safe systemic antifungal exposure in mammals is unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/40164150/" }, { "review_event_id": "IRD-20261003-B08-10", "object_id": "CIDM-WORK-1924", "pmid": "42202423", "year": 2026, "title": "Drivers of and implementation strategies for influenza vaccination for cardiovascular populations in China: a scoping review", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Scoping review", "research_question": "What drives influenza-vaccine uptake among people with cardiovascular disease in China and which implementation strategies have been used?", "methods_summary": "Academic databases, Chinese trial registry and grey literature were searched through August 2025; 13 publications were mapped to the AAAQ framework.", "main_finding": "Lower socioeconomic status and health literacy were associated with lower uptake; physician recommendation, accessible clinics and reliable supply facilitated vaccination. Multi-domain implementation strategies appeared more effective.", "limitations": "Only 13 heterogeneous publications; scoping review cannot quantify intervention effect reliably.", "cidm_contribution": "Direct CIDM-PH contribution through Rong Liu.", "contradictions_unknowns": "High-quality trials of integrated vaccination strategies in Chinese cardiovascular populations remain sparse.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/42202423/" }, { "review_event_id": "IRD-20261003-B08-11", "object_id": "CIDM-WORK-1925", "pmid": "42153394", "year": 2026, "title": "Voriconazole therapy and CYP2C19 phenotype: identifying patients who may need alternative antifungal therapy", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Multicentre retrospective pharmacogenomic cohort", "research_question": "Does CYP2C19 phenotype predict switching from voriconazole and identify patients requiring atypical dosing?", "methods_summary": "194 adults from three Sydney hospitals with prior voriconazole use and therapeutic drug monitoring underwent later CYP2C19 genotyping; records were audited for exposure, adverse effects and switching.", "main_finding": "Switching occurred in 32% and was not associated with CYP2C19 phenotype. However, all ultrarapid metabolizers on 400 mg/day had subtherapeutic concentrations; higher doses were needed for therapeutic exposure.", "limitations": "Retrospective design; poor-metabolizer subgroup was very small and treatment decisions occurred without genotype data.", "cidm_contribution": "Westmead/CIDM fungal pharmacotherapy and precision-medicine contribution.", "contradictions_unknowns": "Prospective genotype-guided dosing studies are needed to quantify clinical benefit beyond therapeutic drug monitoring alone.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13184621/" }, { "review_event_id": "IRD-20261003-B08-12", "object_id": "CIDM-WORK-1926", "pmid": "41628075", "year": 2026, "title": "Knowledge gaps and research priorities to understand sex differences in immunity", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Scientific essay / research-priority synthesis", "research_question": "Which mechanistic gaps prevent biological sex differences in immunity from being translated into sex-tailored prevention and treatment?", "methods_summary": "Expert essay synthesizing evidence on sex chromosomes, sex steroids, immune-cell pathways, disease-specific mechanisms and study-design limitations.", "main_finding": "Robust sex differences in immunity are well documented, but the cell-specific and disease-specific mechanisms remain insufficiently resolved for routine sex-tailored care.", "limitations": "Perspective/essay rather than systematic review or primary experiment; priorities reflect expert synthesis.", "cidm_contribution": "Direct CIDM affiliation through Katie Flanagan.", "contradictions_unknowns": "Mechanistic interactions among chromosomes, hormones, age, microbiota and environment remain a central unresolved problem.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12863523/" }, { "review_event_id": "IRD-20261003-B08-13", "object_id": "CIDM-WORK-1927", "pmid": "42718495", "year": 2026, "title": "Grand challenges in sex differences in immunology: problems the field must solve before biological sex can guide clinical practice", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Grand-challenge perspective", "research_question": "What major research problems must be solved before sex-differential immunology can guide clinical practice?", "methods_summary": "Expert synthesis organized around six mechanistic and translational challenges.", "main_finding": "The paper highlights lifespan immune-cell differences, X/Y-linked genes and X-inactivation, sex steroids/epigenetics, microbiota interactions, appropriate experimental design and translation into sex-tailored prevention/treatment.", "limitations": "Agenda-setting perspective, not evidence that sex-tailored clinical interventions are already validated.", "cidm_contribution": "Direct CIDM affiliation through Katie Flanagan.", "contradictions_unknowns": "Clinical thresholds for when sex-specific mechanisms justify different treatment remain undeveloped.", "confidence": "HIGH", "source_url": "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2026.1965393/full" }, { "review_event_id": "IRD-20261003-B08-14", "object_id": "CIDM-WORK-1928", "pmid": "42704229", "year": 2026, "title": "A randomized controlled trial of cefiderocol versus standard therapy for Gram-negative bacterial bloodstream infections: Benefit and risk assessment using DOOR and generalized pairwise comparisons", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Secondary composite-outcome analysis of randomized controlled trial", "research_question": "Does integrating efficacy, safety and functional outcomes change the assessment of cefiderocol versus standard care in Gram-negative bloodstream infection?", "methods_summary": "Prespecified DOOR and generalized-pairwise-comparison analyses of the GAME CHANGER randomized trial, including a carbapenem-resistant subset.", "main_finding": "Cefiderocol was not superior to standard care: DOOR probability 50.4% in the main population; GPC win ratio 1.04. Results were also not superior in the carbapenem-resistant subset.", "limitations": "Secondary composite-endpoint analysis; weights/order of components and limited resistant-subset size influence precision.", "cidm_contribution": "Direct CIDM-PH/CIDM clinical-trial lineage through GAME CHANGER investigators.", "contradictions_unknowns": "Which resistant phenotypes or patient subgroups derive differential benefit remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/42704229/" }, { "review_event_id": "IRD-20261003-B08-15", "object_id": "CIDM-WORK-1929", "pmid": "42569662", "year": 2026, "title": "Impact and effectiveness of Australia's 2025 hybrid RSV immunisation program: results from the PAEDS-FluCAN Network", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "National prospective test-negative case-control effectiveness study", "research_question": "How effective and impactful was Australia's 2025 hybrid maternal-vaccine/nirsevimab RSV program against infant hospitalization?", "methods_summary": "Thirteen PAEDS-FluCAN hospitals enrolled 3,743 children in 2025; 2,719 were RSV-positive and 1,024 test-negative controls. Adjusted test-negative effectiveness and year-to-year hospitalization impact were estimated.", "main_finding": "Overall effectiveness against RSV hospitalization in the newborn cohort was 82.6%; maternal vaccine effectiveness was 81.5% and nirsevimab 89.6%. Hospitalizations fell most in infants under 3 months.", "limitations": "Impact comparison used one pre-program year and excluded two states with prior nirsevimab programs; observational effectiveness is subject to residual confounding.", "cidm_contribution": "Australian paediatric respiratory-infection surveillance contribution within the expanded CIDM network.", "contradictions_unknowns": "Sustained multi-season effectiveness, year-round impact and changing RSV epidemiology require continued monitoring.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/42569662/" }, { "review_event_id": "IRD-20261003-B08-16", "object_id": "CIDM-WORK-1930", "pmid": "37848057", "year": 2023, "title": "Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Population genomic surveillance study", "research_question": "What evolutionary patterns and lineage replacements were captured by three years of population-representative SARS-CoV-2 surveillance?", "methods_summary": "Sequenced community samples from the ONS COVID-19 Infection Survey, April 2020–March 2023, were analysed for lineage growth, divergence, diversity and viral burden.", "main_finding": "Successive lineages underwent sweeps or partial sweeps with growth advantages; between-lineage evolution occurred faster than within-lineage evolution, while average viral burden declined from mid-2021.", "limitations": "Sampling and sequencing success changed through time; observed sweeps reflect both viral biology and population immunity.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to large-scale viral genomic epidemiology.", "contradictions_unknowns": "How future immune landscapes alter the tempo of lineage replacement remains unpredictable.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37848057/" }, { "review_event_id": "IRD-20261003-B08-17", "object_id": "CIDM-WORK-1931", "pmid": "37796091", "year": 2023, "title": "Ultrasensitive PCR system for HBV DNA detection: Risk stratification for occult hepatitis B virus infection in English blood donors", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Diagnostic assay-development / blood-safety study", "research_question": "Can ultrasensitive HBV DNA testing improve identification and risk stratification of occult HBV among anti-HBc-positive donors?", "methods_summary": "Seven extraction methods and three PCR assays were compared; the optimized method used 5 mL plasma and was applied to anti-HBc-positive blood donations.", "main_finding": "The system detected around 0.5 IU/mL HBV DNA and increased detection among anti-HBc-positive donors from 0.5% to 1.9%. Higher anti-HBc titre and absent anti-HBs predicted DNA positivity.", "limitations": "Very low prevalence leads to small numbers of DNA-positive donors; clinical infectivity of all low-level positives is not directly demonstrated.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to blood-borne-virus diagnostics and safety.", "contradictions_unknowns": "Best thresholds for retaining donors while minimizing transfusion risk require policy-specific modelling.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37796091/" }, { "review_event_id": "IRD-20261003-B08-18", "object_id": "CIDM-WORK-1932", "pmid": "37578971", "year": 2023, "title": "Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Population-representative viral-load modelling study", "research_question": "How are age, vaccination and SARS-CoV-2 variant associated with within-host viral burden after correcting for time-since-infection sampling bias?", "methods_summary": "ONS Infection Survey Ct distributions were bias-adjusted and analysed using partial least squares regression.", "main_finding": "Vaccination reduced viral burden by an estimated 67%; viral burden increased 17% per 10 years of age; among vaccinated people, Delta burden was markedly higher than Alpha.", "limitations": "Ct-derived viral burden and statistical bias correction rely on model assumptions; viral burden is not identical to infectiousness.", "cidm_contribution": "Tanya Golubchik contribution to population-scale SARS-CoV-2 quantitative epidemiology.", "contradictions_unknowns": "Variant effects are intertwined with changing immunity and cannot be generalized unchanged to later variants.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37578971/" }, { "review_event_id": "IRD-20261003-B08-19", "object_id": "CIDM-WORK-1933", "pmid": "37403889", "year": 2023, "title": "Postpandemic rebound of adeno-associated virus type 2 (AAV2) infections temporally associated with an outbreak of unexplained severe acute hepatitis in children in the United Kingdom", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Molecular epidemiology / wastewater surveillance", "research_question": "Did AAV2 circulation rebound after pandemic restrictions and temporally coincide with the unexplained paediatric hepatitis outbreak?", "methods_summary": "300 paediatric respiratory samples from pre-pandemic and 2022 periods plus wastewater from 50 London locations were tested by PCR and sequencing.", "main_finding": "AAV2 detection was sevenfold higher in 2022 than 2009–2013 (10% vs 1.4%), especially in adenovirus-positive samples; wastewater AAV2 rose sharply in early 2022.", "limitations": "Temporal association does not prove AAV2 caused hepatitis; respiratory and wastewater sampling are indirect measures of paediatric liver disease.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to post-pandemic viral ecology and genomic surveillance.", "contradictions_unknowns": "The causal role of AAV2, helper viruses and host susceptibility in severe hepatitis remains unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37403889/" }, { "review_event_id": "IRD-20261003-B08-20", "object_id": "CIDM-WORK-1934", "pmid": "37367727", "year": 2023, "title": "Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy", "access_level": "FULL_TEXT", "scientific_review_state": "FULL_TEXT_REVIEWED", "study_type": "Cross-sectional HIV drug-resistance genomics", "research_question": "How often does dolutegravir resistance emerge among treatment-experienced patients with virological failure in Northeast Nigeria?", "methods_summary": "61 failing-treatment participants were sampled; after sequencing/QC, 33 complete HIV genomes were analysed for drug-resistance mutations.", "main_finding": "NRTI and NNRTI resistance was common, but only 1/33 had dolutegravir-associated resistance mutations, supporting a high resistance barrier for dolutegravir despite virological failure.", "limitations": "Small final genomic sample, cross-sectional design and no direct adherence data; persistent viraemia may have been driven largely by poor adherence.", "cidm_contribution": "Tanya Golubchik contribution through the PANGEA genomic consortium.", "contradictions_unknowns": "Longer-term population surveillance is needed because prolonged failure under imperfect adherence can still select INSTI resistance.", "confidence": "HIGH", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10393879/" }, { "review_event_id": "IRD-20261003-B09-01", "object_id": "CIDM-WORK-1935", "pmid": "37231004", "year": 2023, "title": "COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Population behavioural epidemiology study", "research_question": "Did COVID-19 vaccination lead individuals or populations to increase social contacts or other risk-related behaviours?", "methods_summary": "UK population behavioural/contact data were analysed while accounting for changing mitigation policies and vaccination levels.", "main_finding": "Individual vaccination status was not strongly related to riskier behaviour, but behaviour tracked rising vaccination coverage at the population level, consistent with population-level risk compensation.", "limitations": "Observational behavioural data cannot fully separate vaccination effects from policy changes, pandemic fatigue and other time-varying influences.", "cidm_contribution": "Tanya Golubchik-linked UK population surveillance collaboration; adds behavioural context to vaccine and transmission modelling.", "contradictions_unknowns": "The degree to which population-level risk compensation materially offset vaccine-associated transmission reduction remains uncertain.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37231004/" }, { "review_event_id": "IRD-20261003-B09-02", "object_id": "CIDM-WORK-1936", "pmid": "37193713", "year": 2023, "title": "Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Large population antibody-correlates study", "research_question": "How do booster vaccination and breakthrough infection differ in antibody trajectories and protection against Omicron BA.4/5 reinfection?", "methods_summary": "Antibody trajectories and subsequent infection were analysed in 154,149 UK adults after booster vaccination or breakthrough infection.", "main_finding": "Higher anti-spike antibody levels predicted greater protection. Breakthrough infection provided greater and somewhat longer-lasting protection at a given antibody level than booster vaccination alone.", "limitations": "Observational comparison; infection carries risks that vaccination does not, so greater post-infection protection is not an argument to prefer infection.", "cidm_contribution": "Tanya Golubchik-linked UK population immunity collaboration.", "contradictions_unknowns": "Protection estimates change with variant evolution and background immunity and should not be transferred unchanged to later variants.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37193713/" }, { "review_event_id": "IRD-20261003-B09-03", "object_id": "CIDM-WORK-1937", "pmid": "37738808", "year": 2023, "title": "Socioeconomic disadvantage and engagement with digital contact tracing for COVID-19 in Western Sydney: A secondary analysis of surveillance data", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Secondary surveillance-data analysis", "research_question": "Which demographic and socioeconomic factors were associated with engagement in digital COVID-19 contact tracing in Western Sydney?", "methods_summary": "133,055 positive SARS-CoV-2 cases from August 2021 to February 2022 were linked with digital questionnaire response and area-level disadvantage; logistic regression assessed response predictors.", "main_finding": "Of those issued a questionnaire, 81% responded. Response odds were lower in men, people aged 80+ and residents of the most disadvantaged areas.", "limitations": "Area-level disadvantage may not represent individual circumstances; digital response is influenced by access, literacy and support factors not fully measured.", "cidm_contribution": "Shopna Bag/Western Sydney public-health contribution to equitable digital outbreak response.", "contradictions_unknowns": "How much targeted assistance can close digital-engagement gaps requires intervention evaluation.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37738808/" }, { "review_event_id": "IRD-20261003-B09-04", "object_id": "CIDM-WORK-1938", "pmid": "37719417", "year": 2023, "title": "Bacillus Calmette-Guérin vaccination for protection against recurrent herpes labialis: a nested randomised controlled trial", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Nested randomized controlled trial", "research_question": "Can BCG-Denmark reduce recurrence of frequent herpes labialis through off-target immunomodulatory effects?", "methods_summary": "Nested within BRACE; 84 participants with frequent recurrent cold sores were randomized to BCG or control and followed for 12 months.", "main_finding": "BCG delayed first recurrence by about 1.55 months and reduced recurrence burden in this small subgroup; prespecified subgroup analysis suggested benefit was concentrated in males.", "limitations": "Small nested subgroup with wide uncertainty; self-reported recurrence burden and sex interaction require independent replication.", "cidm_contribution": "Mark W Douglas contribution through the BRACE trial network.", "contradictions_unknowns": "The increased first-episode risk observed among participants without prior cold sores and the sex-specific effect need further study.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37719417/" }, { "review_event_id": "IRD-20261003-B09-05", "object_id": "CIDM-WORK-1939", "pmid": "37648284", "year": 2023, "title": "Polo-like kinase-1 mediates hepatitis C virus-induced cell migration, a drug target for liver cancer", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic cell-biology study", "research_question": "How does HCV infection alter hepatocyte cytoskeletal behaviour and could PLK1 be a target for HCV-associated liver cancer progression?", "methods_summary": "HCV cell-culture models, phosphoproteomic/cytoskeletal analysis, mutational experiments and pharmacologic PLK1 inhibition were used.", "main_finding": "HCV induced β-actin Ser239 phosphorylation through PLK1, increasing cell motility; the PLK1 inhibitor volasertib prevented these changes, supporting a mechanistic link to migration/invasion.", "limitations": "Cell-culture mechanistic evidence does not establish that PLK1 inhibition prevents metastasis or improves HCC outcomes in patients.", "cidm_contribution": "Mark W Douglas/Storr Liver Centre contribution to HCV-associated carcinogenesis mechanisms.", "contradictions_unknowns": "Therapeutic window, timing and clinical efficacy of PLK1 targeting in HCV-related HCC remain unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37648284/" }, { "review_event_id": "IRD-20261003-B09-06", "object_id": "CIDM-WORK-1940", "pmid": "37318059", "year": 2023, "title": "Targeting liver metabolism: a pathway to cure hepatitis B virus?", "access_level": "METADATA", "scientific_review_state": "METADATA_REVIEWED", "study_type": "Editorial / expert commentary", "research_question": "Could host liver-metabolic pathways provide new routes toward functional HBV cure?", "methods_summary": "Editorial/expert commentary; PubMed provides no attributable abstract for scientific-content review.", "main_finding": "The article frames host-targeting metabolic therapy as a potential complement to direct antiviral approaches in pursuit of HBV functional cure.", "limitations": "Editorial, not a primary experiment or systematic review; no efficacy estimate should be inferred.", "cidm_contribution": "Direct Centre for Infectious Diseases and Microbiology affiliation through Mark W Douglas.", "contradictions_unknowns": "Which metabolic targets offer sufficient antiviral benefit without unacceptable host toxicity remains unresolved.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37318059/" }, { "review_event_id": "IRD-20261003-B09-07", "object_id": "CIDM-WORK-1941", "pmid": "37240132", "year": 2023, "title": "PEMT Mediates Hepatitis C Virus-Induced Steatosis, Explains Genotype-Specific Phenotypes and Supports Virus Replication", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Mechanistic lipidomics study", "research_question": "Which host lipid pathway links HCV replication with virus-induced hepatic steatosis?", "methods_summary": "Quantitative lipidomics, subcellular fractionation and HCV cell-culture models were combined with PEMT knockdown experiments.", "main_finding": "HCV increased phosphatidylcholine and other lipids; infection induced PEMT, and PEMT knockdown inhibited viral replication, supporting PEMT as a link between HCV replication and steatosis.", "limitations": "Cell-culture findings require confirmation in human liver disease and therapeutic-target validation.", "cidm_contribution": "Direct CIDM affiliation through Mark W Douglas; host-metabolism mechanism relevant to HCV pathogenesis.", "contradictions_unknowns": "Whether PEMT inhibition can safely reduce HCV-associated metabolic pathology in vivo is unknown.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37240132/" }, { "review_event_id": "IRD-20261003-B09-08", "object_id": "CIDM-WORK-1942", "pmid": "37099341", "year": 2023, "title": "Randomized Trial of BCG Vaccine to Protect against Covid-19 in Health Care Workers", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "International double-blind randomized controlled trial", "research_question": "Does BCG-Denmark reduce symptomatic or severe COVID-19 in SARS-CoV-2-naive healthcare workers?", "methods_summary": "3,988 healthcare workers were randomized to BCG-Denmark or saline and followed for 12 months; the modified intention-to-treat population included 3,386 SARS-CoV-2-naive participants.", "main_finding": "BCG did not reduce symptomatic COVID-19 at 6 months: estimated risk was 14.7% with BCG versus 12.3% with placebo, with no evidence of protective benefit.", "limitations": "Recruitment stopped early because COVID-specific vaccines became available; severe-event numbers were limited.", "cidm_contribution": "Mark W Douglas contribution through the multinational BRACE consortium.", "contradictions_unknowns": "This trial does not support broad BCG protection against COVID-19 in healthcare workers; heterologous effects in other infections remain separate questions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37099341/" }, { "review_event_id": "IRD-20261003-B09-09", "object_id": "CIDM-WORK-1943", "pmid": "37002990", "year": 2023, "title": "Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Variant neutralisation / population-immunity study", "research_question": "How did emerging Omicron sublineages gain a growth advantage despite increasing population antibody breadth?", "methods_summary": "Emerging BQ, BA.2.75 and recombinant Omicron lineages were examined in the context of neutralising-antibody responses and maturing population immunity.", "main_finding": "Distinct Omicron descendants converged on spike changes that improved antibody evasion, supporting immune escape as an important contributor to lineage outgrowth despite broader population immunity.", "limitations": "Variant fitness is multifactorial; neutralisation escape alone does not quantify transmissibility or disease severity.", "cidm_contribution": "Australian SARS-CoV-2 immunology collaboration including Mark W Douglas.", "contradictions_unknowns": "The relative contributions of immune escape, intrinsic transmissibility and changing host immunity vary across lineages and time.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/37002990/" }, { "review_event_id": "IRD-20261003-B09-10", "object_id": "CIDM-WORK-1944", "pmid": "36906180", "year": 2023, "title": "Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Genomic outbreak investigation", "research_question": "How often did hospital discharge seed SARS-CoV-2 outbreaks in Lothian care homes during the first epidemic wave?", "methods_summary": "All 787 hospital-to-care-home discharges from March–May 2020 were reviewed using testing, clinical timelines and whole-genome sequencing.", "main_finding": "776 of 787 discharges were ruled out as sources, 10 were inconclusive, and only one had genomic, temporal and location evidence linking it to a care-home cluster of 10 cases.", "limitations": "Low viral genomic diversity and missing sequence data left some episodes unresolved; results are specific to one region and epidemic phase.", "cidm_contribution": "Tanya Golubchik contribution through COG-UK genomic epidemiology.", "contradictions_unknowns": "The study argues against hospital discharge as the dominant source in this setting but cannot exclude all unobserved introductions.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/36906180/" }, { "review_event_id": "IRD-20261003-B09-11", "object_id": "CIDM-WORK-1945", "pmid": "36752042", "year": 2023, "title": "Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Blood-safety molecular surveillance", "research_question": "Was mpox virus DNA detectable in blood donations during the 2022 outbreak in southern England?", "methods_summary": "454 nucleic-acid-test minipools representing 10,896 unique donors were tested with MPXV-specific and generic orthopoxvirus PCR assays.", "main_finding": "No donor minipool was positive by either assay, providing reassurance that detectable viraemia and transfusion-transmission risk were rare or absent in this donor population.", "limitations": "Blood donors are not representative of the highest-risk population; absence of detected DNA does not prove zero transfusion risk.", "cidm_contribution": "Tanya Golubchik/Sydney ID contribution to blood-safety surveillance.", "contradictions_unknowns": "Risk during outbreaks with different epidemiology or donor-selection policies requires continued surveillance.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/36752042/" }, { "review_event_id": "IRD-20261003-B09-12", "object_id": "CIDM-WORK-1946", "pmid": "36353774", "year": 2023, "title": "High activation levels maintained in receptor-binding domain-specific memory B cells in people with severe coronavirus disease 2019", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Single-cell longitudinal immunology study", "research_question": "Does acute COVID-19 severity leave persistent differences in SARS-CoV-2 RBD-specific memory B-cell states?", "methods_summary": "Single-cell transcriptomic and B-cell receptor analysis compared RBD-specific memory B cells in three people recovering from severe and four from mild/moderate COVID-19 at about two and four months.", "main_finding": "Severe COVID-19 was associated with persistently higher TNF/NF-kB activation and distinct activated memory-B-cell subsets, while both groups showed ongoing somatic hypermutation over time.", "limitations": "Very small sample; molecular signatures require replication and do not by themselves establish better or worse protective immunity.", "cidm_contribution": "Dominic Dwyer/COSIN study-group lineage within Australian COVID-19 immunology.", "contradictions_unknowns": "Whether persistent activation improves memory, reflects dysregulation or predicts long-term symptoms remains unclear.", "confidence": "MEDIUM", "source_url": "https://pubmed.ncbi.nlm.nih.gov/36353774/" }, { "review_event_id": "IRD-20261003-B09-13", "object_id": "CIDM-WORK-1947", "pmid": "41067237", "year": 2026, "title": "Cefiderocol versus standard therapy for hospital-acquired and health-care-associated Gram-negative bacterial bloodstream infection (the GAME CHANGER trial): an open-label, parallel-group, randomised trial", "access_level": "ABSTRACT", "scientific_review_state": "ABSTRACT_REVIEWED", "study_type": "Multinational randomized controlled trial", "research_question": "Is cefiderocol non-inferior or superior to standard-care antibiotics for hospital-acquired or health-care-associated Gram-negative bloodstream infection?", "methods_summary": "513 participants were randomized across 17 tertiary hospitals in six countries; 504 entered the main analysis. The primary endpoint was 14-day all-cause mortality.", "main_finding": "Fourteen-day mortality was 8% with cefiderocol and 7% with standard care (risk difference 1%, 95% CI -3 to 6), meeting non-inferiority but not superiority. In the carbapenem-resistant subset, mortality was 14% versus 10%, with wide uncertainty.", "limitations": "Open-label design; resistant-organism subgroup was relatively small; study was not able to establish superiority.", "cidm_contribution": "Indy Sandaradura as verified GAME CHANGER investigator; direct CIDM clinical-trial lineage.", "contradictions_unknowns": "Which carbapenem-resistant organisms or patient subgroups benefit most from cefiderocol remains unresolved.", "confidence": "HIGH", "source_url": "https://pubmed.ncbi.nlm.nih.gov/41067237/" } ] }