Lancet Microbe最新文献

{"title":"Defining the serotypes of SARS-CoV-2 subvariants up to December, 2024.","authors":"Pei Du, Jiajing Li, Tianxiang Kong, Bin Lu, Ruiqi Li, George Fu Gao, Qihui Wang","doi":"10.1016/j.lanmic.2025.101124","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101124","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101124"},"PeriodicalIF":20.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040079","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":"Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review.","authors":"Yu Lan, Isabel Rancu, Melanie H Chitwood, Benjamin Sobkowiak, Kate Nyhan, Hsien-Ho Lin, Chieh-Yin Wu, Barun Mathema, Tyler S Brown, Caroline Colijn, Joshua L Warren, Ted Cohen","doi":"10.1016/j.lanmic.2025.101094","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101094","url":null,"abstract":"<p><p>Tuberculosis remains a leading cause of infection-related mortality, and efforts to reduce its incidence have been hindered by an incomplete understanding of local Mycobacterium tuberculosis transmission dynamics. Advances in pathogen sequencing and spatial analysis have created new opportunities to map M tuberculosis transmission patterns more precisely. In this scoping review, we searched for studies combining pathogen genetics and location data to analyse the spatial patterns of M tuberculosis transmission and identified 142 studies published between 1994 and 2024. Secular changes in genetic methods were observed, with genome sequencing approaches largely replacing lower-resolution genotyping methods since 2020. The included studies addressed four primary research questions: how are tuberculosis cases and M tuberculosis transmission clusters geographically distributed; do spatially concentrated M tuberculosis clusters exist, and where are these areas located; when spatial concentration occurs, what host, pathogen, or environmental factors contribute to these patterns; and do identifiable relationships exist between the spatial proximity of tuberculosis cases and the genetic similarity of the M tuberculosis isolates infecting these individuals? Collectively, in this Review, we examined the available study data, evaluated the analytical requirements for addressing these questions, and discussed opportunities and challenges for future research. We found that the integration of spatial and genomic data can inform a detailed understanding of local M tuberculosis transmission patterns, but improved study designs and new analytical methods to address gaps in sampling completeness and to integrate additional movement data are needed to fully realise the potential of these tools.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101094"},"PeriodicalIF":20.9,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024431","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":"UK launch metagenomic pathogen surveillance programme.","authors":"Priya Venkatesan","doi":"10.1016/j.lanmic.2025.101143","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101143","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101143"},"PeriodicalIF":20.9,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057457","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":"Hepatitis B virus resistance to nucleos(t)ide analogue therapy: WHO consultation on questions, challenges, and a roadmap for the field.","authors":"Sheila F Lumley, Jolynne Mokaya, Tongai G Maponga, Anna Kramvis, Geoffrey Dusheiko, William Irving, Marion Delphin, Khadija Said Mohammed, Louise O Downs, Elizabeth Waddilove, Motswedi Anderson, Collins Iwuji, Nokukhanya Msomi, Ponsiano Ocama, Saeed Hamid, Danjuma Adda, Rachel Halford, Kenneth Kabagambe, Kimberley S M Benschop, Seth Inzaule, Polin Chan, Margaret Alia Samson Paul, Kiyohiko Izumi, Tiara Nisa, Jean De Dieu Iragena, Amalia Girón-Callejas, Aboudou Raïmi Kpossou, Ganiyu Jamiyu, Omolara Emmanuel, Mahamadou Balkissa, Mamadou Keita, Nishi Prabdial-Sing, Alexander Martinez, Eleanor Namusoke Magongo, Yiming Shao, Omar Sued, Leandro Soares Sereno, Robert W Shafer, Olufunmilayo Lesi, Diana Faini, Philippa Easterbrook, Chris Duncombe, Michael R Jordan, Philippa C Matthews","doi":"10.1016/j.lanmic.2025.101076","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101076","url":null,"abstract":"<p><p>In this Review, we summarise outputs from a multidisciplinary consultation convened by WHO between July 11 and 13, 2023, to discuss hepatitis B virus (HBV) drug resistance (HBVDR). Treatment of chronic HBV infection with highly effective nucleos(t)ide analogue agents, tenofovir and entecavir, is a crucial intervention that supports the global goal of elimination of HBV infection as a public health threat. The risk of HBVDR as a threat to treatment outcomes is currently considered low from a public health perspective; however, drug resistance can influence individual outcomes, particularly among those who are treatment-experienced. We highlight the need to develop appropriate prevention, monitoring, and surveillance approaches for HBVDR, to support investment in the global scale-up of HBV diagnosis and treatment. Recommendations for the HBVDR field will ultimately be incorporated into a WHO integrated Global Action Plan for drug-resistant HIV, viral hepatitis, and priority sexually transmitted infections.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101076"},"PeriodicalIF":20.9,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144062749","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":"The fate of tuberculosis programmes without USAID.","authors":"Talha Burki","doi":"10.1016/j.lanmic.2025.101145","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101145","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101145"},"PeriodicalIF":20.9,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988972","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 spread of clade Ib mpox: a growing concern.","authors":"Ashutosh Pareek, Runjhun Singhal, Aaushi Pareek, Anil Chuturgoon, Vasso Apostolopoulos, Vijay Kumar Chattu","doi":"10.1016/j.lanmic.2025.101132","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101132","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101132"},"PeriodicalIF":20.9,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024418","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":"Altered IL-6 signalling and risk of tuberculosis.","authors":"Jian Huang, Zheng-Fu Xie","doi":"10.1016/j.lanmic.2025.101134","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101134","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101134"},"PeriodicalIF":20.9,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006733","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":"Evaluating the performance of common reference laboratory tests for acute dengue diagnosis: a systematic review and meta-analysis of RT-PCR, NS1 ELISA, and IgM ELISA.","authors":"Kamla Pillay, Suzanne H Keddie, Elizabeth Fitchett, Cassandra Akinde, Oliver Bärenbold, John Bradley, Jane Falconer, Ruth H Keogh, Zhia Ning Lim, Behrouz Nezafat Maldonado, Laura Maynard-Smith, Ellen Sugrue, Okuda Taylor, Heidi Hopkins, Audrey Dubot-Pérès","doi":"10.1016/j.lanmic.2025.101088","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101088","url":null,"abstract":"<p><strong>Background: </strong>Dengue fever is listed among the top ten global health threats by WHO. Prompt identification of dengue virus can guide clinical management and outbreak response, yet laboratory diagnosis is complex, costly, and lacks consensus on performance evaluation. This systematic review aims to provide reliable diagnostic accuracy estimates in order to inform global guidance and evaluate novel rapid diagnostic tests.</p><p><strong>Methods: </strong>In this systematic review and meta-analysis, we searched nine literature databases on Feb 16, 2021, for reports on five common reference tests for dengue infection: NS1 ELISA, IgM ELISA, IgG ELISA, RT-PCR, and viral neutralisation test. Articles were included if they reported primary data from more than five participants to complete 2×2 tables comparing one of these tests (on human serum) with any comparator. Diagnostic accuracy was estimated using Bayesian random-effect meta-analysis, which does not require a gold-standard comparator. Risk of bias was assessed using QUADAS-2. This review is registered with PROSPERO (CRD42022341552).</p><p><strong>Findings: </strong>Data were extracted from 161 articles, allowing analysis of multiple timeframes for three tests of interest. Pooled sensitivities of RT-PCR (0-4 days after symptom onset), NS1 ELISA (0-4 days), and IgM ELISA (1-7 days) were 95% (95% credible interval 77-99), 90% (68-98), and 71% (57-84), respectively. The corresponding pooled estimates of specificity were 89% (60-98), 93% (71-99), and 91% (82-95). A subanalysis of only studies at low risk of bias demonstrated similar estimates.</p><p><strong>Interpretation: </strong>IgM ELISA shows poor diagnostic accuracy early in the symptom course. NS1 ELISA shows similar diagnostic accuracy to RT-PCR, which has important implications for global public health policy, given its relatively low cost and accessibility.</p><p><strong>Funding: </strong>None.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101088"},"PeriodicalIF":20.9,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019971","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":"Multidimensional analysis of MERS-CoV infection in Jordan and the Arabian Peninsula.","authors":"Linfeng Wang, Zhiwen Wang","doi":"10.1016/j.lanmic.2025.101078","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101078","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101078"},"PeriodicalIF":20.9,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024301","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":"Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.","authors":"Ouli Xie, Rebecca H Chisholm, Leo Featherstone, An N T Nguyen, Andrew J Hayes, Magnus G Jespersen, Cameron Zachreson, Nefel Tellioglu, Gerry Tonkin-Hill, Ravindra Dotel, Stephanie Spring, Alice Liu, Alexander Rofe, Sebastian Duchene, Norelle L Sherry, Robert W Baird, Vicki L Krause, Deborah C Holt, Lachlan J M Coin, Neela Joshi Rai, Matthew V N O'Sullivan, Katherine Bond, Jukka Corander, Benjamin P Howden, Tony M Korman, Bart J Currie, Steven Y C Tong, Mark R Davies","doi":"10.1016/j.lanmic.2024.101053","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101053","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from five hospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream S pyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Findings: &lt;/strong&gt;We identified 500 cases of invasive S pyogenes infection in patients in the Top End and 495 cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5·97 (95% CI 4·61-7·73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5·41, 4·28-6·89). The odds of in-hospital mortality (OR 0·43, 95% CI 0·26-0·70), 30-day mortality (0·38, 0·23-0·63), and ICU admission (0·42, 0·30-0·59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 S pyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hype","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101053"},"PeriodicalIF":20.9,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804344","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}