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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 articleAtchison CJ, Gilby N, Pantelidou G, et al., 2025,
Strategies to Increase Response Rate and Reduce Nonresponse Bias in Population Health Research: Analysis of a Series of Randomized Controlled Experiments during a Large COVID-19 Study.
, JMIR Public Health Surveill, Vol: 11BACKGROUND: High response rates are needed in population-based studies, as nonresponse reduces effective sample size and bias affects accuracy and decreases the generalizability of the study findings. OBJECTIVE: We tested different strategies to improve response rate and reduce nonresponse bias in a national population-based COVID-19 surveillance program in England, United Kingdom. METHODS: Over 19 rounds, a random sample of individuals aged 5 years and older from the general population in England were invited by mail to complete a web-based questionnaire and return a swab for SARS-CoV-2 testing. We carried out several nested randomized controlled experiments to measure the impact on response rates of different interventions, including (1) variations in invitation and reminder letters and SMS text messages and (2) the offer of a conditional monetary incentive to return a swab, reporting absolute changes in response and relative response rate (95% CIs). RESULTS: Monetary incentives increased the response rate (completed swabs returned as a proportion of the number of individuals invited) across all age groups, sex at birth, and area deprivation with the biggest increase among the lowest responders, namely teenagers and young adults and those living in more deprived areas. With no monetary incentive, the response rate was 3.4% in participants aged 18-22 years, increasing to 8.1% with a £10 (US $12.5) incentive, 11.9% with £20 (US $25.0), and 18.2% with £30 (US $37.5) (relative response rate 2.4 [95% CI 2.0-2.9], 3.5 [95% CI 3.0-4.2], and 5.4 [95% CI 4.4-6.7], respectively). Nonmonetary strategies had a modest, if any, impact on response rate. The largest effect was observed for sending an additional swab reminder (SMS text message or email). For example, those receiving an additional SMS text message were more likely to return a completed swab compared to those receiving the standard email-SMS approach, 73.3% versus 70.2%: percentage difference 3.1%
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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 articleSun D, Ellepola G, Herath J, et al., 2025,
Climatically Specialized Lineages of Batrachochytrium dendrobatidis, and its Likely Asian Origins
, EcoHealth, ISSN: 1612-9202Chytridiomycosis is a wildlife disease that has caused significant declines in amphibian populations and species extinctions worldwide. Asia, where the causal pathogens Batrachochytrium dendrobatidis (Bd) and B. salamndrivorans (Bsal) originated, has not witnessed mass die-offs. It is hypothesized that Asian amphibians may have evolved immunity to clinical Batrachochytrium infection, but this has not been explored in depth due to limited knowledge of endemic lineages and infection patterns. We investigated Bd’s genetic diversity and infection patterns in south China’s Guangxi region using the internal transcribed spacer (ITS) marker and nested PCR. Across the 17 forest sites studied (N = 1088 individuals; 1012 adults and 76 tadpoles), the overall prevalence of Bd infection was 4.74% in adult individuals and 5.26% in tadpoles. We found seven new haplotypes, four of which were closely related to the BdASIA-1 lineage from South Korea. The most prevalent haplotype (genetically similar to BdASIA-3) was found in 11 out of 15 infected species, including a salamander with non-lethal skin lesions. A generalized linear model of our environmental data indicates that Bd infection is correlated with mean temperature of the warmest quarter and elevation, with higher infection prevalence associated with lower temperature and relatively higher elevation in southern China. Our findings suggest significant undiscovered genetic diversity of Asian Bd lineages in this region. Longer-term studies are required to further investigate Bd diversity, prevalence, seasonality, and impact on native species and populations in Southern China and across the region of origin in Asia.
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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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Journal articleWariri O, Utazi CE, Okomo U, et al., 2025,
Multi-level determinants of timely routine childhood vaccinations in The Gambia: Findings from a nationwide analysis.
, Vaccine, Vol: 43INTRODUCTION: Achieving the ambitious goals of the Immunisation Agenda 2030 (IA2030) requires a deeper understanding of factors influencing under-vaccination, including timely vaccination. This study investigates the demand- and supply-side determinants influencing the timely uptake of key childhood vaccines scheduled throughout the first year of life in The Gambia. METHODS: We used two nationally-representative datasets: the 2019-20 Gambian Demographic and Health Survey and the 2019 national immunisation facility mapping. Using Bayesian multi-level binary logistic regression models, we identified key factors significantly associated with timely vaccination for five key vaccines: birth dose of hepatitis-B (HepB0), first, second, and third doses of the pentavalent vaccine (Penta1, Penta2, Penta3), and first-dose of measles-containing vaccine (MCV1) in children aged 12-35 months. We report the adjusted Odds Ratios (aORs) and 95 % Credible Intervals (95 % CIs) in each case. RESULTS: We found that demand-side factors, such as ethnicity, household wealth status, maternal education, maternal parity, and the duration of the household's residency in its current location, were the most common drivers of timely childhood vaccination. However, supply-side factors such as travel time to the nearest immunisation clinic, availability of cold-storage and staffing numbers in the nearest immunisation clinic were also significant determinants. Furthermore, the determinants varied across specific vaccines and the timing of doses. For example, delivery in a health facility (aOR = 1.58, 95 %CI: 1.02-2.53), living less than 30 min (aOR = 2.11, 95 %CI: 1.2-8.84) and living between 30 and 60 min (aOR = 3.68, 95 %CI: 1.1-14.99) from a fixed-immunisation clinic was associated with timely HepB0, a time-sensitive vaccine that must be administered within 24 h of birth. On the other hand, children who received Penta1 and
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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 articleOliveira LMA, Costa NS, Mestrovic T, et al., 2025,
The battle against antimicrobial resistance is more important now than ever: time to educate, advocate and act
, International Journal of Infectious Diseases, Vol: 150, ISSN: 1201-9712 -
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: 0278-0062 -
Journal articlePagabeleguem S, Da DF, Somé BM, et al., 2025,
Near-infrared spectroscopy discriminates mass-reared sterile and wild tsetse flies.
, PLoS Negl Trop Dis, Vol: 19BACKGROUND: Monitoring the efficacy of the sterile insect technique (SIT) programs, it is desirable to discriminate between wild and sterile tsetse males captured in monitoring traps. Currently, this is primarily achieved by marking sterile males with fluorescent dye powder before release, and identifying them using a fluorescence camera and/or microscope. However, the accuracy of this method is limited due to defective marking and wild flies contaminated with a few dye particles in the monitoring traps. Molecular techniques have been developed to discriminate doubtful flies, but they are expensive for endemic countries. METHODOLOGY/PRINCIPAL FINDINGS: Here, we investigate the ability of a new generation monitoring tool, Near-Infrared Spectroscopy (NIRS), to discriminate between laboratory-reared Glossina palpalis gambiensis males and their field counterparts. NIRS was able to discriminate wild males from laboratory-reared males with 86% accuracy. Notably, the prediction accuracy improved to 88% when the laboratory-reared flies had been irradiated. CONCLUSIONS/SIGNIFICANCE: These findings suggest that NIRS can successfully identify tsetse flies even when UV camera identification is inconclusive. However, further studies are needed to expand the training dataset and include additional environmental variables before validating NIRS as a complementary method for future tsetse eradication programs.
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