Lancet Microbe最新文献

{"title":"Global diversity and evolution of Salmonella enterica serovar Panama: a genomic epidemiology study.","authors":"Caisey V Pulford, Blanca M Perez-Sepulveda, Danielle J Ingle, Rebecca J Bengtsson, Rebecca J Bennett, Ella V Rodwell, Maria Pardos de la Gandara, Charlotte E Chong, P Malaka De Silva, Magali Ravel, Véronique Guibert, Elisabeth Njamkepo, Neil Hall, Marie A Chattaway, Benjamin P Howden, Deborah A Williamson, Jay C D Hinton, François-Xavier Weill, Kate S Baker","doi":"10.1016/j.lanmic.2025.101150","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101150","url":null,"abstract":"<p><strong>Background: </strong>Non-typhoidal Salmonella is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some non-typhoidal Salmonella serovars can also colonise typically sterile sites in people to cause invasive non-typhoidal Salmonella disease. Salmonella enterica serovar Panama is responsible for a substantial number of cases of human bloodstream infection, but despite its global dissemination, numerous outbreaks, and a reported association with invasive non-typhoidal Salmonella disease, S enterica serovar Panama (S Panama) is understudied. We aimed to describe the genomic epidemiology and evolutionary history of S Panama to provide a vital baseline of understanding for this globally important serovar.</p><p><strong>Methods: </strong>In this genomic epidemiology study, we analysed S Panama genomes derived from historical collections, national surveillance datasets, and publicly available epidemiological and whole-genome sequencing data which span the years 1931-2019. Maximum likelihood and Bayesian phylodynamic approaches were used to investigate population structure and evolutionary history and to infer geotemporal dissemination. A combination of different bioinformatic approaches with short-read and long-read data were used to characterise geographical and clade-specific trends in antimicrobial resistance (AMR) and genetic markers for invasiveness.</p><p><strong>Findings: </strong>We analysed 836 S Panama genomes, of which 559 (67%) were sequenced as part of this study. The collection represents all inhabited continents and includes isolates collected between 1931 and 2019. We identified the presence of four geographically linked S Panama clades (C1 [ie, the Latin America and the Caribbean clade; n=338], C2 [ie, the European clade; n=124], C3 [ie, the Martinique clade; n=131], and C4 [ie, the Asia and Oceania clade; n=104]) and regional trends in AMR profiles. Most isolates (715 [86%] of 836) were pan-susceptible to antibiotics and belonged to clades circulating in Latin America and the Caribbean (64%, n=458). Most antibiotic-resistant isolates in our collection (113 [93%] of 121) fell within clades C4 (ie, the Asia and Oceania clade) and C2 (ie, the European clade), the latter of which had the highest invasiveness index values based on the conservation of 196 extraintestinal predictor genes.</p><p><strong>Interpretation: </strong>This first large-scale phylogenetic analysis of S Panama has revealed important information about the population structure, AMR, global ecology, and genetic markers of invasiveness of the identified genomic subtypes. Our findings provide an important baseline for understanding S Panama infection. The presence of multidrug-resistant clades with elevated invasiveness index values should be monitored through ongoing surveillance, as such clades could pose an increased public health risk.</p><p><strong>Funding: </strong>UK Research and Innovation Global Chall","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101150"},"PeriodicalIF":20.4,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review.","authors":"Monika Moir, Nikita Sitharam, Laura Marije Hofstra, Graeme Dor, Gaspary Mwanyika, Yajna Ramphal, Martina L Reichmuth, James Emmanuel San, Robert Gifford, Eduan Wilkinson, Derek Tshiabuila, Wolfgang Preiser, Abla Ahouefa Konou, Molalegne Bitew, Anyebe Bernard Onoja, Giacomo Maria Paganotti, Adugna Abera, James Ayei Maror, John Kayiwa, Sara Abuelmaali, Eddy Kinganda Lusamaki, Marietjie Venter, Felicity Burt, Cheryl Baxter, Richard Lessells, Tulio de Oliveira, Houriiyah Tegally","doi":"10.1016/j.lanmic.2025.101176","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101176","url":null,"abstract":"<p><p>West Nile virus (WNV) is a priority pathogen that poses a high risk for public health emergencies of global concern. Although WNV is endemic to Africa, only few (n=63) whole genomic sequences are available from the continent. In this Review, we examined the status of the molecular testing and genomic sequencing of WNV across Africa and mapped its global spatiotemporal spread. WNV has been detected in 39 African countries, the Canary Islands, and Réunion Island. Although publications, including those with molecular data, originated from 24 of these countries, genomic sequences were available from only 16 countries. Our analysis identified regions with detected viral circulation but without molecular surveillance. The current literature has substantial knowledge gaps in terms of the disease burden, molecular epidemiology, and distribution of WNV in Africa. Addressing these gaps requires an integrated One Health surveillance approach, which is challenging to establish. We propose three key surveillance needs that could improve the current understanding of the WNV disease burden in Africa, to strengthen the global public health response to this vector-borne disease.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101176"},"PeriodicalIF":20.4,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Severe acute respiratory syndrome (SARS) mathematical models and disease parameters: a systematic review.","authors":"Christian Morgenstern, Thomas Rawson, Isobel Routledge, Mara Kont, Natsuko Imai-Eaton, Janetta Skarp, Patrick Doohan, Kelly McCain, Rob Johnson, H Juliette T Unwin, Tristan Naidoo, Dominic P Dee, Kanchan Parchani, Bethan N Cracknell Daniels, Anna Vicco, Kieran O Drake, Paula Christen, Richard J Sheppard, Sequoia I Leuba, Joseph T Hicks, Ruth McCabe, Rebecca K Nash, Cosmo N Santoni, Gina Cuomo-Dannenburg, Sabine van Elsland, Sangeeta Bhatia, Anne Cori","doi":"10.1016/j.lanmic.2025.101144","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101144","url":null,"abstract":"<p><p>SARS-CoV-1 was the first documented coronavirus to cause an acute epidemic in humans and remains a priority pathogen owing to the risk of re-emergence. Robust estimates of key epidemiological parameters are essential to guide outbreak responses and inform mathematical models. Existing systematic reviews have been limited in scope, warranting a comprehensive and up-to-date review. We conducted a systematic review (PROSPERO CRD42023393345) of studies of severe acute respiratory syndrome (SARS) transmission models and parameters characterising the transmission, evolution, natural history, severity, risk factors, and seroprevalence of SARS-CoV-1. Information was extracted using a custom database and quality assessment tool. We extracted data on 519 parameters, 243 risk factors, and 112 models from 289 papers. We found that SARS is characterised by high lethality (case-fatality ratio, 10·9%), transmissibility (R₀ range, 1·1-4·59), and superspreading events (approximately 91% of SARS-CoV-1 infections can be attributed to 20% of individuals who were most infectious). Infection risk was the highest among health-care workers and close contacts of infected individuals. Severe disease and death were associated with age and existing comorbidities. The natural history of SARS was poorly characterised, except for the incubation and mean onset-to-hospitalisation delays. The extracted data were compiled into our associated R package, epireview, which can be updated to incorporate novel findings, thus providing a key resource for informing response to future coronavirus outbreaks. By making data accessible through an updatable database, we support rapid, evidence-informed responses to potential re-emergence of SARS-CoV-1 or related coronaviruses.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101144"},"PeriodicalIF":20.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and public health implications of persistent SARS-CoV-2 infection in a person with HIV disease.","authors":"Frances V Ue, Paul E Sax","doi":"10.1016/j.lanmic.2025.101205","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101205","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101205"},"PeriodicalIF":20.9,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond bacteria: a multikingdom ecological perspective on neonatal gut and severe viral lower respiratory tract infection risk.","authors":"Jiaqi Wang, Zengguo Cao, Xuemin Jin","doi":"10.1016/j.lanmic.2025.101202","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101202","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101202"},"PeriodicalIF":20.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Duck-origin H5N6 avian influenza threatens public health: a challenge for poultry vaccination in China.","authors":"Zhen Wang, Xi Cheng, Jinhua Liu, Yipeng Sun","doi":"10.1016/j.lanmic.2025.101203","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101203","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101203"},"PeriodicalIF":20.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mycoplasma pneumoniae: re-emergence and beyond.","authors":"Patrick M Meyer Sauteur","doi":"10.1016/j.lanmic.2025.101191","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101191","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101191"},"PeriodicalIF":20.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global emergence and transmission dynamics of carbapenemase-producing Citrobacter freundii sequence type 22 high-risk international clone: a retrospective, genomic, epidemiological study.","authors":"Qiaojun Wang, Longjie Zhou, Xiaoling Chen, Jiayao Yao, Xinran Sun, Kai Peng, Yanyun Gao, Edward J Feil, Yunsong Yu, Zhiqiang Wang, Ruichao Li, Xi Li","doi":"10.1016/j.lanmic.2025.101149","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101149","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Carbapenemase-producing Citrobacter (CPC) species have recently been recognised as emerging pathogens associated with nosocomial infections in humans. The increased rate of Citrobacter freundii infections is a public health concern and there is a paucity of genomic data regarding its global transmission dynamics. We aimed to characterise the genetic features of CPC species, and their associated carbapenemase-encoding plasmids, obtained from hospitalised patients in China and from publicly available global data, with a particular focus on high-risk clones.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This was a retrospective, genomic epidemiological study of CPC species obtained from a tertiary hospital in Zhejiang Province, China, from March 5, 2013, to March 5, 2023. We used antimicrobial susceptibility testing, short-read and long-read whole-genome sequencing, phylogenomic analysis, and plasmid structure analysis. A global dataset of complete plasmid sequences encoding bla&lt;sub&gt;KPC&lt;/sub&gt;, bla&lt;sub&gt;NDM&lt;/sub&gt;, and bla&lt;sub&gt;IMP&lt;/sub&gt; was constructed from the National Center for Biotechnology Information (NCBI) RefSeq database to provide insights into their diversity and distribution. All carbapenemase-producing Citrobacter freundii genomes from the NCBI GenBank database were incorporated in the comparative genomic analyses. Bayesian phylogeographical analysis and growth rate assays were carried out to characterise the high-risk C freundii sequence type (ST) 22 clone.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Findings: &lt;/strong&gt;1724 Citrobacter species isolates were collected from diverse clinical specimens, with 48 identified as CPC species. Citrobacter koseri (22 [46%] of 48) and C freundii (20 [42%]) were the predominant CPC species. Comparative analysis found C freundii carried significantly higher median numbers of plasmid replicons (5·0 [IQR 3·3-6·0] vs 2·0 [2·0-3·0]; p&lt;0·0001) and acquired antimicrobial resistance genes (12·0 [7·3-15·8] vs 3·0 [3·0-5·3]; p&lt;0·0001) than did C koseri. Molecular characterisation identified Inc-type plasmids, In823::Kl.pn.I3/In1589-like/In837-like integrons, Tn6296/Tn125/Tn5060 transposons, and insertion sequences (eg, IS26, IS3000, IS5, ISAba125, ISCR1), collectively facilitating the dissemination of carbapenemase genes. Global analysis of 3126 carbapenemase-encoding plasmids found epidemic plasmids with broad host ranges and global diversity. Phylogenetic investigation of predominant carbapenemase-encoding plasmids showed their persistence across geographical regions, temporal spans, and Enterobacterales species, exhibiting high genetic similarity to our clinical plasmids. A phylogenetic tree of 726 global carbapenemase-producing C freundii genomes showed that ST22 (227 [31·3%]) represents the predominant multidrug-resistant clone across community, health-care, and environmental niches. Transmission across continents contributes to the global predominance of the ST22 clone, which carries a high load of resistance genes (m","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101149"},"PeriodicalIF":20.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing the use of bacteriophages to tackle AMR.","authors":"Timothy Jesudason","doi":"10.1016/j.lanmic.2025.101204","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101204","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101204"},"PeriodicalIF":20.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Blood RNA biomarkers and C-reactive protein for triage of adult patients with tuberculosis lymphadenitis and pericarditis in South Africa: a single-centre, prospective, observational, diagnostic accuracy study.","authors":"Tiffeney Mann, Stephanie Minnies, Rishi K Gupta, Byron W P Reeve, Georgina Nyawo, Zaida Palmer, Charissa Naidoo, Anton Doubell, Alfonso Pecoraro, Thadathilankal-Jess John, Pawel Schubert, Claire J Calderwood, Aneesh Chandran, Grant Theron, Mahdad Noursadeghi","doi":"10.1016/j.lanmic.2025.101153","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101153","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Data on the diagnostic accuracy of blood RNA biomarker signatures for extrapulmonary tuberculosis are scarce. We aimed to address this question among people investigated for tuberculosis lymphadenitis and tuberculosis pericarditis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This prospective, observational, diagnostic accuracy study was done at a tertiary hospital in Cape Town, South Africa. We enrolled consecutive symptomatic adults (aged 18 years or older) with presumptive tuberculosis lymphadenitis (Jan 25, 2017, to Oct 9, 2019) or tuberculosis pericarditis (Nov 24, 2016, to Oct 28, 2019). We used microbiological testing of samples from the site of disease as the reference standard. We evaluated the diagnostic accuracy of seven previously reported blood RNA signatures by area under the receiver operating characteristic curve (AUROC) and sensitivity and specificity at prespecified thresholds using two SDs above the mean of a healthy reference control group, benchmarked against blood C-reactive protein and WHO target product profile for a tuberculosis triage test. Decision curve analysis was used to evaluate clinical utility of the best-performing blood RNA signature and C-reactive protein.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Findings: &lt;/strong&gt;The pooled cohort included 440 individuals, 374 of whom (275 with lymphadenitis and 99 with pericarditis) had at least one microbiological test from the site of disease, blood C-reactive protein, and RNA measurements available and were included in the analysis. 181 (48%) participants were female and 193 (52%) were male. The diagnostic accuracy of blood RNA signatures was similar across patients with lymphadenitis and pericarditis. In pooled analysis of both cohorts, all RNA signatures had similar discrimination, with AUROC point estimates ranging from 0·77 (95% CI 0·72-0·82) to 0·82 (0·77-0·86), and greater than that of C-reactive protein (0·61 [0·56-0·67]). The best-performing signature (Roe3) did not meet the WHO target product profile benchmark for a triage test. At the prespecified threshold, Roe3 had 78% (95% CI 72-83) sensitivity and 69% (62-75) specificity; C-reactive protein at a threshold of 10 mg/L had 83% (77-87) sensitivity and 35% (29-43) specificity. In this setting, decision curve analysis showed that Roe3 offered greater net benefit than other approaches for services aiming to reduce the number needed to investigate with confirmatory testing to fewer than four to identify each individual with tuberculosis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Interpretation: &lt;/strong&gt;Our results suggest RNA biomarkers show better accuracy and clinical utility than C-reactive protein to trigger confirmatory tuberculosis testing in patients with tuberculosis lymphadenitis and tuberculosis pericarditis, but still fall short of the WHO target product profile for tuberculosis triage tests.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Funding: &lt;/strong&gt;South African Medical Research Council, European and Developing Countries Clinical Trials Partnership 2, National In","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101153"},"PeriodicalIF":20.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}