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Journal articleHan SM, Kubo Y, Robert A, et al., 2025,
Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients.
, Viruses, Vol: 17Numerous studies have documented the evidence of virus-virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV-RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups-elderly individuals (>64 years old) and school-aged children (6-18 years old)-were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09-3.06) and 1.38 (95% CI: 1.01-1.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available i
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Journal articleAnanth S, Adeoti AO, Ray A, et al., 2025,
Healthcare worker views on antimicrobial resistance in chronic respiratory disease
, Antimicrobial Resistance and Infection Control, Vol: 14, ISSN: 2047-2994Background and objectiveAntimicrobial resistance (AMR) is a global crisis, however, relatively little is known regarding its impact in chronic respiratory disease and the specific challenges faced by healthcare workers across the world in this field. We aimed to assess global healthcare worker views on the challenges they face regarding AMR in chronic respiratory disease.MethodsAn online survey was sent to healthcare workers globally working in chronic respiratory disease through a European Respiratory Society clinical research collaboration (AMR-Lung) focussed on AMR in chronic lung disease. Responses from different geographic regions were analysed.Results279 responses were received across 60 countries. 54.5% of respondents encountered AMR in chronic respiratory disease weekly. There were differences in perceived high-priority diseases and species with AMR burden between Europe, Asia and Africa. 76.4% of respondents thought that inappropriate antimicrobial prescribing in chronic respiratory disease was common. However, only 43.4% of respondents thought that there were adequate antimicrobial stewardship programmes in their area for chronic respiratory disease, with limited availability in outpatient (29.0%) and ambulatory settings (24.7%). Developing rapid diagnostics for antimicrobial susceptibility (59.5%) was perceived to be the most common challenge in implementing antimicrobial stewardship, with an improved understanding of regional epidemiology of AMR strains the most important factor to improve outcome (55.2%).ConclusionsAMR has significant perceived burden in chronic respiratory disease by healthcare professionals globally. However, current implementation of antimicrobial stewardship is limited, with significant challenges related to the availability of rapid diagnostics and understanding of regional epidemiology of AMR strains.
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Journal articleLansbury L, McKeever TM, Lawrence H, et al., 2025,
Pneumococcal pneumonia trends in adults hospitalised with community-acquired pneumonia over 10 years (2013-2023) and the role of serotype 3.
, Thorax, Vol: 80, Pages: 86-96BACKGROUND: With higher valency pneumococcal vaccines on the horizon and new adult immunisation strategies under discussion, we aimed to evaluate the contribution of individual pneumococcal serotypes to the burden of pneumococcal community-acquired pneumonia (CAP). Over 10 years, trends in pneumococcal pneumonia epidemiology in adults hospitalised with CAP were assessed. The risk factors and severity associated with serotype 3 were examined. METHODS: We conducted a prospective cohort study of adults hospitalised with CAP between September 2013 and May 2023. Pneumococcal serotypes were identified using a serotype-specific 24-valent urinary-antigen assay. Trends in the proportion of CAP due to pneumococcus and causative serotypes were compared prepandemic and postpandemic. Risk factors and severity of serotype 3 pneumonia were compared with other serotypes using logistic regression. RESULTS: Of 5186 patients with CAP, 2193 (42.2%) had pneumococcal pneumonia. The proportion of CAP due to pneumococcus increased across all ages between 2013 and 2023 (36.4%-66.9%, p<0.001). The proportion due to serotype 3 increased significantly from 13.4% (2013) to 48.8% (2023). Serotype 3 pneumonia in adults was associated with older age (p<0.001), male sex (adjusted OR (aOR) 2.22, 95% CI 1.64 to 3.01) and chronic renal disease (aOR 1.81, 95% CI 1.09 to 3.02). Serotype 3 pneumonia was not observed to be associated with severity, critical care requirement, mortality or readmission. INTERPRETATION: Serotype 3 is the predominant serotype in adult pneumococcal CAP and has been increasing despite a mature infant pneumococcal immunisation programme, consistent with a lack of herd protection for this serotype.
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Journal articleNikitin D, Whittles LK, Imai-Eaton JW, et al., 2025,
Cost-effectiveness of 4CMenB vaccination against gonorrhea: importance of dosing schedule, vaccine sentiment, targeting strategy, and duration of protection
, Journal of Infectious Diseases, Vol: 231, Pages: 71-83, ISSN: 0022-1899BackgroundObservational evidence suggests the 4CMenB meningococcal vaccine may partially protect against gonorrhea, with 1 dose being two-thirds as protective as 2 doses. We examined the cost-effectiveness of vaccinating men who have sex with men (MSM) in England, with 1- or 2-dose primary vaccination.MethodsIntegrated transmission-dynamic health-economic modeling explored the effects of targeting strategy, first- and second-dose uptake levels, and duration of vaccine protection, using observational estimates of vaccine protection.ResultsVaccination with 1 or 2 primary doses is always cost-saving, irrespective of uptake, although vaccine sentiment is an important determinant of impact and cost-effectiveness. The most impactful and cost-effective targeting is offering “vaccination according to risk” (VaR), to all patients with gonorrhea plus those reporting high numbers of sexual partners. If VaR is not feasible to implement then the more restrictive strategy of “vaccination on diagnosis” (VoD) with gonorrhea is cost-effective, but much less impactful. Under conservative assumptions, VaR (2-dose) saves £7.62M (95% credible interval [CrI], 1.15–17.52) and gains 81.41 (95% CrI, 28.67–164.23) quality-adjusted life-years (QALYs) over 10 years; VoD (2-dose) saves £3.40M (95% CrI, .48–7.71) and gains 41.26 (95% CrI, 17.52–78.25) QALYs versus no vaccination. Optimistic versus pessimistic vaccine-sentiment assumptions increase net benefits by approximately 30% (VoD) or approximately 60% (VaR).ConclusionsAt UK costs, targeted 4CMenB vaccination of MSM gains QALYs and is cost-saving at any uptake level. Promoting uptake maximizes benefits and is an important role for behavioral science.
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Journal articleMurray KA, 2025,
Keep it in the ground: climate change could prompt the reemergence of zombie pathogens.
, BMJ, Vol: 388 -
Journal articleStrepis N, Dollee D, Vrins D, et al., 2025,
BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows
, BMC Genomics, Vol: 26 -
Journal articleVoller C, Perrin LD, Gibbens JC, et al., 2025,
Can biosecurity on farms reduce bovine tuberculosis risks in cattle in England? A review of observational and literature-based evidence
, Veterinary Record, Vol: 196, ISSN: 0042-4900Background: Bovine tuberculosis (TB) is a burden to cattle farming in Great Britain. Poor biosecurity has been identified as contributing to the epidemic. Methods: We conducted a systematic review of epidemiological studies published in the scientific literature between 1921 and 2024 that measured the association between farm biosecurity and cattle TB. Eligible studies controlled for confounding factors and reported statistically significant association/s between biosecurity and TB (p < 0.05) and/or an effect ratio/s of more than 3. Biosecurity uptake in England was assessed using official Disease Report Forms (DRFs) from 4074 TB incidents occurring in 2018 and 2019. Results: Thirty-three papers with 116 effect estimates met the inclusion criteria and were grouped according to a five-point biosecurity plan. There was consistent evidence for TB risk being reduced by reducing contact with neighbouring herds and preventing cattle at higher TB risk from entering herds. The evidence for the effectiveness of measures for reducing contact between badgers and cattle was inconsistent. The DRF data showed a low uptake of biosecurity to reduce contact between badgers and cattle. Limitations: All the studies identified were retrospective. Biosecurity was measured using different instruments, for example, questionnaires. Conclusions: There is analytical epidemiological evidence supporting guidance for improving biosecurity, but there are some limitations. Further research is needed to identify the most effective wildlife-focused measures.
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Journal articleJorgensen D, Grassly NC, Pons Salort M, 2025,
Global age-stratified seroprevalence of enterovirus D68: a systematic literature review
, The Lancet Microbe, Vol: 6, ISSN: 2666-5247Enterovirus D68 (EV-D68), first isolated in 1962, emerged in 2014, causing outbreaks of severe respiratory infections and acute flaccid myelitis. In this systematic review, we have compiled all available literature on age-stratified seroprevalence estimates of EV-D68. Ten studies from six countries were retained, all conducted using microneutralisation assays, despite wide variations in protocols and challenge viruses. The age profiles of seroprevalence were similar across time and regions; seroprevalence increased quickly with age, reaching roughly 100% by the age of 20 years and with no sign of decline throughout adulthood. This suggests continuous or frequent exposure of the populations to the virus, or possible cross-reactivity with other viruses. Studies with two or more cross-sectional surveys reported consistently higher seroprevalence at later timepoints, suggesting a global increase in transmission over time. This systematic review concludes that standardising serological protocols, understanding the contribution of cross-reactivity with other pathogens to the high reported seroprevalence, and quantifying individual exposure to EV-D68 over time are the main research priorities for the future.
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Journal articleLiu C, Cheng S, Shi M, et al., 2025,
IMITATE: clinical prior guided hierarchical vision-language pre-training
, IEEE Transactions on Medical Imaging, Vol: 44, Pages: 519-529, ISSN: 0278-0062In medical Vision-Language Pre-training (VLP), significant work focuses on extracting text and image features from clinical reports and medical images. Yet, existing methods may overlooked the potential of the natural hierarchical structure in clinical reports, typically divided into ‘findings’ for description and ‘impressions’ for conclusions. Current VLP approaches tend to oversimplify these reports into a single entity or fragmented tokens, ignoring this structured format. In this work, we propose a novel clinical prior guided VLP framework named IMITATE to learn the structure information from medical reports with hierarchical vision-language alignment. The framework derives multi-level visual features from the chest X-ray (CXR) images and separately aligns these features with the descriptive and the conclusive text encoded in the hierarchical medical report. Furthermore, a new clinical-informed contrastive loss is introduced for cross-modal learning, which accounts for clinical prior knowledge in formulating sample correlations in contrastive learning. The proposed model, IMITATE, outperforms baseline VLP methods across six different datasets, spanning five medical imaging downstream tasks. Experimental results show benefits of using hierarchical structures in medical reports for VLP. Code: https://github.com/cheliu-computation/IMITATE-TMI2024.
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Journal articleGrassly N, Shaw AG, Owusu M, 2025,
Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges
, The Lancet Microbe, Vol: 6, ISSN: 2666-5247Wastewater surveillance holds great promise as a sensitive method to detect spillover of zoonotic infections and early pandemic emergence, thereby informing risk mitigation and public health response. Known viruses with pandemic potential are shed in human stool or urine, or both, and the experiences with SARS-CoV-2, monkeypox virus, and Zika virus highlight the feasibility of community-based wastewater surveillance for pandemic viruses that have different transmission routes. We reviewed human shedding and wastewater surveillance data for prototype viruses representing viral families of concern to estimate the likely sensitivity of wastewater surveillance compared with that of clinical surveillance. We examined how data on wastewater surveillance detection, together with viral genetic sequences and animal faecal biomarkers, could be used to identify spillover infections or early human transmission and adaptation. The opportunities and challenges associated with global wastewater surveillance for the prevention of pandemics are described in this Personal View, focusing on low-income and middle-income countries, where the risk of pandemic emergence is the highest. We propose a research and public health agenda to ensure an equitable and sustainable solution to these challenges.
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