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Journal articleCholsaktrakool P, Kawang K, Sangpiromapichai N, et al., 2025,
Inference of Antimicrobial Resistance (AMR) from a Whole Genome Database Outperforming AMR Gene Detection
, iScience, Pages: 112962-112962, ISSN: 2589-0042 -
Journal articleDe Nardi A, Marini G, Dorigatti I, et al., 2025,
Quantifying West Nile virus circulation in the avian host population in Northern Italy.
, Infect Dis Model, Vol: 10, Pages: 375-386West Nile virus (WNV) is one of the most threatening mosquito-borne pathogens in Italy where hundreds of human cases were recorded during the last decade. Here, we estimated the WNV incidence in the avian population in the Emilia-Romagna region through a modelling framework which enabled us to eventually assess the fraction of birds that present anti-WNV antibodies at the end of each epidemiological season. We fitted an SIR model to ornithological data, consisting of 18,989 specimens belonging to Corvidae species collected between 2013 and 2022: every year from May to November birds are captured or shot and tested for WNV genome presence. We found that the incidence peaks between mid-July and late August, infected corvids seem on average 17% more likely to be captured with respect to susceptible ones and seroprevalence was estimated to be larger than other years at the end of 2018, consistent with the anomalous number of recorded human infections. Thanks to our modelling study we quantified WNV infection dynamics in the corvid community, which is still poorly investigated despite its importance for the virus circulation. To the best of our knowledge, this is among the first studies providing quantitative information on infection and immunity in the bird population, yielding new important insights on WNV transmission dynamics.
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Journal articlePeeling RW, Fongwen NT, Guzman MG, et al., 2025,
Specimen and data sharing to advance research and development on Zika virus
, The Lancet Microbe, Vol: 6, Pages: 101057-101057, ISSN: 2666-5247 -
Journal articleDuchêne DA, Chowdhury A-A, Yang J, et al., 2025,
Drivers of avian genomic change revealed by evolutionary rate decomposition
, Nature, Vol: 641, Pages: 1208-1216, ISSN: 0028-0836Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1,2,3,4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous–Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
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Journal articlePapadopoulou E, Sykes DL, Goeminne P, et al., 2025,
Patients’ perspectives on antimicrobial resistance in chronic respiratory disease: an AMR-Lung – European Lung Foundation global patient survey
, ERJ Open Research, ISSN: 2312-0541Background:Antimicrobial resistance (AMR) represents a significant global health threat, particularly for people with chronic respiratory diseases. However, their experiences, knowledge, priorities and concerns have not been comprehensively assessed. This study aimed to gauge patients’ perspectives of AMR burden in chronic respiratory disease.Methods:An anonymous web-based patient survey was developed by AMR-Lung ERS Clinical Research Collaboration and members from the European Lung Foundation patient advisory groups, consisting of 39 questions, translated into 20 languages and held online over a 2-month period. Multivariable logistic regression analyses were used to explore disease-specific burden and factors potentially affecting AMR across different healthcare settings.Results:Among 2012 respondents from 57 countries on all 6 continents, 30.7% recalled having an AMR-associated infection, while 12.6% perceived their last antimicrobial course as ineffective. 30.5% received long-term prophylactic antimicrobials, with 44.6% of them recalling an AMR-associated infection. 17.6% reported antimicrobial use without medical prescription, while 9.5% perceived prescriptions as delayed. Respondents recognised mostly their healthcare professionals as an information source regarding AMR, but 27% were unaware of AMR prior to the survey. Patients from high-income countries were more likely to be knowledgeable about AMR, and less inclined to use antimicrobials without prescription and to perceive them as ineffective. Respondents overwhelmingly viewed AMR as a personal (76.4%) and global (79.6%) threat.Conclusions:This global large-scale survey ascertains for the first time the high AMR burden from the perspective of people with chronic respiratory diseases, accentuating the need to promote AMR awareness, judicious antimicrobial use, and accessibility to quality healthcare.
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Journal articleWhitaker M, Rodrigues S, Cooke G, et al., 2025,
How COVID-19 affected academic publishing: a three-year study of 17 million research papers
, International Journal of Epidemiology, ISSN: 0300-5771 -
Journal articleGregson S, Moorhouse L, Maswera R, et al., 2025,
Gender Norms and Structural Barriers to Use of HIV Prevention in Unmarried and Married Young Women in Manicaland, Zimbabwe: An HIV Prevention Cascade Analysis
, Gates Open Research, Vol: 8, Pages: 22-22<ns3:p>Background Gender norms against adolescent girls and young women (AGYW)’s having pre-marital sex and using condoms in marriage are included as barriers to motivation to use condoms in HIV prevention cascades. Representative data on gender norms are needed to test this assumption. Methods General-population survey participants in Manicaland, Zimbabwe (ages≥15, N=9803) reported agreement/disagreement with statements on gender norms. AGYW at risk of HIV infection reported whether community views discouraged condom use. Multivariable logistic regression was used to measure associations between AGYW’s perceiving negative gender norms and condom HIV prevention cascades. Results 57% of men and 70% of women disagreed that ‘If I have a teenage daughter and she has sex before marriage, I would be ok with this’; and 41% of men and 57% of women disagreed that ‘If I have a teenage daughter, I would tell her about condoms’. 32% and 69% of sexually-active HIV-negative unmarried AGYW, respectively, said negative community views were important in their decisions to use condoms and their friends were not using condoms. In each case, those who agreed had lower motivation to use condoms. Fewer unmarried AGYW with friends not using condoms used condoms themselves (39% <ns3:italic>vs.</ns3:italic> 68%; age- and site-adjusted odds ratios (aOR)=0.29, 95%CI, 0.15-0.55). 21% of men and 32.5% of women found condom use in marriage acceptable. 74% and 93% of married AGYW at risk, respectively, said negative community views influenced their decisions to use condoms and their friends did not use condoms. Fewer married AGYW reporting friends not using condoms were motivated to use condoms but no difference was found in their own condom use (4.1% <ns3:italic>vs.</ns3:italic> 6.9%; aOR=0.57, 95%CI, 0.08-2.66). Conclusions Negative gender norms can form a barrier to motivation to use condoms in unmarried and married AGYW at r
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Journal articleDan S, Ling Z, Chen Y, et al., 2025,
Addressing survey fatigue bias in longitudinal social contact studies to improve pandemic preparedness
, Scientific Reports, Vol: 15, ISSN: 2045-2322Social contact surveys are an important tool to assess infection risks within populations, and the effect of non-pharmaceutical interventions on social behaviour during disease outbreaks, epidemics, and pandemics. Numerous longitudinal social contact surveys were conducted during the COVID-19 era, however data analysis is plagued by survey fatigue, a phenomenon whereby the average number of social contacts reported declines with the number of repeat participations and as participants’ engagement decreases over time. Using data from the German COVIMOD Study between April 2020 to December 2021, we demonstrate that survey fatigue varied considerably by sociodemographic factors and was consistently strongest among parents reporting children contacts (parental proxy reporting), students, middle-aged individuals, those in full-time employment and those self-employed. We find further that, when using data from first-time participants as gold standard, statistical models incorporating a simple logistic function to control for survey fatigue were associated with substantially improved estimation accuracy relative to models with no survey fatigue adjustments, and that no cap on the number of repeat participations was required. These results indicate that existing longitudinal contact survey data can be meaningfully interpreted under an easy-to-implement statistical approach addressing survey fatigue confounding, and that longitudinal designs including repeat participants are a viable option for future social contact survey designs.
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Journal articleSlavinska A, Jauneikaite E, Meškytė U, et al., 2025,
Genomic characterization of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021
, Microbial Genomics, Vol: 11, ISSN: 2057-5858Listeria monocytogenes is a saprophytic gram-positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania, and up to 20 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterization of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021 : 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, 5 (7.1%) from wounds, 1 (1.4%) from pleural fluid and 1 (1.4%) from a brain abscess. Two phylogenetic lineages were identified—I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)—along with three serogroups—IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2) and singletons for ST37, ST451 and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6–48 core SNPs from reference and 0, 4 or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights
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Journal articleRomanello M, Beggs PJ, Cai W, et al., 2025,
From crisis to opportunity: a united response to Trump's attacks on climate action
, Lancet, Vol: 405, Pages: 1647-1650, ISSN: 0140-6736
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