Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101201
Magdalena Medrzycki PhD , Richard A Stanton PhD , Danielle A Rankin PhD , Sam Horwich-Scholefield MPH , Arif Mahmud DrPH , Tyler Maruca MS , Sarah Brister MPH , Lian Hsiao MPH , Elisabeth Vaeth MPH , Michelle Therrien MS , Erin L Young PhD , Kelly F Oakeson PhD , Farhana Haque MS , Lindsay Neff BS , Alison Laufer Halpin PhD , Sarah Sabour PhD , Jennifer Y Huang MPH , Stephen P LaVoie PhD , Maroya Spalding Walters PhD
Background
Most US carbapenem-resistant Acinetobacter baumannii (CRAB) isolates harbour carbapenem-hydrolysing class D β-lactamases. Other carbapenemases, such as New Delhi metallo-β-lactamase (NDM), are uncommon but emerging. We describe the epidemiology of NDM-producing CRAB reported to the US Centers for Disease Control and Prevention (CDC).
Methods
We defined cases as A baumannii with blaNDM confirmed by molecular testing and isolated from any specimen source from a patient in the USA between Oct 1, 2013, and March 31, 2022, and passively reported to the CDC from regional, state, local public health, and CDC laboratories. Epidemiologically linked cases had epidemiological linkage (eg, overlapping health-care facility stay) with one or more other cases. We assessed case relatedness through analysis of whole-genome sequence data using traditional multilocus sequence typing (MLST; Oxford scheme [sequence typeOX]) and core genome MLST. To understand the potential origins of NDM-CRAB in the USA, we compared sequences of cases to US CRAB without NDM and to NDM-CRAB from non-US locations.
Findings
We identified 327 NDM-CRAB cases from 264 patients in 21 US states. Among patients with available epidemiological information, 192 (90%) of 214 had epidemiological linkage to at least one additional case and 13 (7%) of 193 were hospitalised outside the USA 12 months or less before index specimen collection. Five regionally distinct sequence type clusters were identified among the 264 case patients; three (sequence type OX218, sequence type OX281, and sequence type OX1697) were closely related to international NDM-CRAB isolates.
Interpretation
We identified regionally distinct NDM-CRAB strains, suggesting localised transmission in the USA. Some NDM-CRAB strains in the USA are closely related to strains identified outside the USA, suggesting that spread followed importation.
{"title":"New Delhi metallo-β-lactamase-producing Acinetobacter baumannii in the USA from October, 2013, to March, 2022: a retrospective molecular epidemiological analysis","authors":"Magdalena Medrzycki PhD , Richard A Stanton PhD , Danielle A Rankin PhD , Sam Horwich-Scholefield MPH , Arif Mahmud DrPH , Tyler Maruca MS , Sarah Brister MPH , Lian Hsiao MPH , Elisabeth Vaeth MPH , Michelle Therrien MS , Erin L Young PhD , Kelly F Oakeson PhD , Farhana Haque MS , Lindsay Neff BS , Alison Laufer Halpin PhD , Sarah Sabour PhD , Jennifer Y Huang MPH , Stephen P LaVoie PhD , Maroya Spalding Walters PhD","doi":"10.1016/j.lanmic.2025.101201","DOIUrl":"10.1016/j.lanmic.2025.101201","url":null,"abstract":"<div><h3>Background</h3><div>Most US carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) isolates harbour carbapenem-hydrolysing class D β-lactamases. Other carbapenemases, such as New Delhi metallo-β-lactamase (NDM), are uncommon but emerging. We describe the epidemiology of NDM-producing CRAB reported to the US Centers for Disease Control and Prevention (CDC).</div></div><div><h3>Methods</h3><div>We defined cases as <em>A baumannii</em> with <em>bla</em><sub>NDM</sub> confirmed by molecular testing and isolated from any specimen source from a patient in the USA between Oct 1, 2013, and March 31, 2022, and passively reported to the CDC from regional, state, local public health, and CDC laboratories. Epidemiologically linked cases had epidemiological linkage (eg, overlapping health-care facility stay) with one or more other cases. We assessed case relatedness through analysis of whole-genome sequence data using traditional multilocus sequence typing (MLST; Oxford scheme [sequence type<sub>OX</sub>]) and core genome MLST. To understand the potential origins of NDM-CRAB in the USA, we compared sequences of cases to US CRAB without NDM and to NDM-CRAB from non-US locations.</div></div><div><h3>Findings</h3><div>We identified 327 NDM-CRAB cases from 264 patients in 21 US states. Among patients with available epidemiological information, 192 (90%) of 214 had epidemiological linkage to at least one additional case and 13 (7%) of 193 were hospitalised outside the USA 12 months or less before index specimen collection. Five regionally distinct sequence type clusters were identified among the 264 case patients; three (sequence type <sub>OX</sub>218, sequence type <sub>OX</sub>281, and sequence type <sub>OX</sub>1697) were closely related to international NDM-CRAB isolates.</div></div><div><h3>Interpretation</h3><div>We identified regionally distinct NDM-CRAB strains, suggesting localised transmission in the USA. Some NDM-CRAB strains in the USA are closely related to strains identified outside the USA, suggesting that spread followed importation.</div></div><div><h3>Funding</h3><div>None.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101201"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145802150","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101203
Zhen Wang , Xi Cheng , Jinhua Liu , Yipeng Sun
{"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":"10.1016/j.lanmic.2025.101203","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101203"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101208
Annaleise R Howard-Jones , Dominic E Dwyer , Bart J Currie , Jen Kok
{"title":"Understanding the virological complexity and importance of One Health surveillance for zoonotic flaviviruses","authors":"Annaleise R Howard-Jones , Dominic E Dwyer , Bart J Currie , Jen Kok","doi":"10.1016/j.lanmic.2025.101208","DOIUrl":"10.1016/j.lanmic.2025.101208","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101208"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144973769","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101194
Byung Uk Lee
{"title":"New aerosol terminology in the transmission of pathogens","authors":"Byung Uk Lee","doi":"10.1016/j.lanmic.2025.101194","DOIUrl":"10.1016/j.lanmic.2025.101194","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101194"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144576620","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101233
Thomas Hänscheid MD , Sara Mahomed MD , Laila Oliveira PhD , Danielle Segóvia Pereira MSc , Prof Martin P Grobusch FRCP
Acid-fast stains (AFS) remain indispensable in modern diagnostic microbiology; they are used for detecting mycobacteria (including Mycobacterium tuberculosis and Mycobacterium leprae), acid-fast parasites, and some acid-variable bacteria as well as in histopathology. Fluorescent AFS surpass brightfield AFS (Ziehl–Neelsen) in sensitivity, particularly when pathogen loads are low. However, latest evidence suggests that these stains target nucleic acids, whereas lipid-rich, intact cell walls merely prevent decolourisation; this evidence corrects the long-held assumption that AFS bind to mycolic acids. This mechanism explains morphological features, such as the characteristic beading in mycobacteria, with direct implications for training microscopists and advancing artificial intelligence-assisted image analysis. This mechanism also facilitates protocol enhancements, including the use of high-yield fluorochromes or novel approaches to reduce background fluorescence. The latest novel applications, such as the detection of a low number of Schistosoma spp eggs, exemplify the broader utility of AFS. Combined with artificial intelligence-based slide interpretation, these advances in understanding staining mechanisms and expanding diagnostic applications show that AFS remain an important diagnostic laboratory modality, with considerable potential for future improvements.
{"title":"Fluorescent acid-fast stains for diagnosing mycobacteria and beyond: back to the future?","authors":"Thomas Hänscheid MD , Sara Mahomed MD , Laila Oliveira PhD , Danielle Segóvia Pereira MSc , Prof Martin P Grobusch FRCP","doi":"10.1016/j.lanmic.2025.101233","DOIUrl":"10.1016/j.lanmic.2025.101233","url":null,"abstract":"<div><div>Acid-fast stains (AFS) remain indispensable in modern diagnostic microbiology; they are used for detecting mycobacteria (including <em>Mycobacterium tuberculosis</em> and <em>Mycobacterium leprae</em>), acid-fast parasites, and some acid-variable bacteria as well as in histopathology. Fluorescent AFS surpass brightfield AFS (Ziehl–Neelsen) in sensitivity, particularly when pathogen loads are low. However, latest evidence suggests that these stains target nucleic acids, whereas lipid-rich, intact cell walls merely prevent decolourisation; this evidence corrects the long-held assumption that AFS bind to mycolic acids. This mechanism explains morphological features, such as the characteristic beading in mycobacteria, with direct implications for training microscopists and advancing artificial intelligence-assisted image analysis. This mechanism also facilitates protocol enhancements, including the use of high-yield fluorochromes or novel approaches to reduce background fluorescence. The latest novel applications, such as the detection of a low number of <em>Schistosoma</em> spp eggs, exemplify the broader utility of AFS. Combined with artificial intelligence-based slide interpretation, these advances in understanding staining mechanisms and expanding diagnostic applications show that AFS remain an important diagnostic laboratory modality, with considerable potential for future improvements.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101233"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145369001","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101231
Martin Kammel , Christoph Buchta , Stephan W Aberle , Stephanie Bligh , Roman Fried , Andrea Griesmacher , Nicole Mastai , Ingo Schellenberg , Nathalie Weiss , Patricia Kaiser , Anika Zimmermann , Martin Obermeier
{"title":"Detection of H5N1 clade 2.3.4.4b in external quality assessment programmes: a pandemic preparedness initiative","authors":"Martin Kammel , Christoph Buchta , Stephan W Aberle , Stephanie Bligh , Roman Fried , Andrea Griesmacher , Nicole Mastai , Ingo Schellenberg , Nathalie Weiss , Patricia Kaiser , Anika Zimmermann , Martin Obermeier","doi":"10.1016/j.lanmic.2025.101231","DOIUrl":"10.1016/j.lanmic.2025.101231","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101231"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114690","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}
<div><h3>Background</h3><div>Parasites are foundational to ecosystem health both as indicator species of community productivity and as drivers of diversity. In bacterial communities, bacteriophage viruses can have such roles as they track and modulate the dynamic composition of bacterial hosts within an ecosystem. We aimed to test whether viromes can be used as broad signatures of microbiome health using previously published results across systems.</div></div><div><h3>Methods</h3><div>In this systematic review and meta-analysis, we searched PubMed, Google Scholar, Scopus, and Web of Science from Jan 22, 2022, to Sept 17, 2024, for peer-reviewed, primary literature published in English, using search terms “phage diversity”, “microbiome”, “virome”, “virus”, “phageome”, “disease”, and “dysbiosis”. Inclusion criteria were: a comparison between a dysbiosis state and a healthy state in a human or animal host; a defined host organism and microbiome site; examination of the virome; an obtained measure of virome diversity (α, β, or both); use of statistical analysis to assess whether α or β diversity are changed in dysbiosis; and sufficient methodology description on viral isolation and on virus sequence analysis pipeline. We conducted a qualitative data analysis to assess factors explaining changes to virome diversity in dysbiosis. We then calculated response ratios for each study to test for overall patterns of virome α diversity change under disturbance. Finally, we conducted a quantitative analysis on studies from which we were able to obtain paired virome and bacteriome α diversity data to examine the correlation between these data in defined health compared with defined disturbance conditions. This study was not registered.</div></div><div><h3>Findings</h3><div>We identified a total of 74 studies for inclusion that spanned human (n=61), mouse (n=8), pig (n=3), dog (n=1), and cow (n=1) hosts and a diverse spectrum of infections and diseases. By comparing observed phage and bacterial diversity in microbiomes characterised by dysbiosis with those considered control populations, we were able to identify some key commonalities. Of the 69 studies that investigated changes to α diversity of the virome in dysbiosis, 28 (41%) reported significant changes, but with variable directional change. Of 38 datasets (from 30 studies) for which virome α diversity values were available, 22 (58%) gave a response ratio of less than 1 (α diversity decreases in dysbiosis) and 16 (42%) of more than 1 (α diversity increases in dysbiosis); however, in 27 (71%) datasets, 95% CIs overlapped with 1 (ie, no change in α diversity). We found shifting virome composition to be a more consistent signature of dysbiosis, with 47 (69%) of 68 studies reporting a significant change in viral β diversity with dysbiosis. 62 (89%) of 70 studies reported significant enrichment of system-specific viral taxa under dysbiosis. Our quantitative correlation analysis suggested that bacterial α diversi
{"title":"Evaluation of bacteriophages as a signature of microbiome health: a systematic review and meta-analysis","authors":"Rachel M Wheatley PhD , Dominique Holtappels PhD , Britt Koskella PhD","doi":"10.1016/j.lanmic.2025.101196","DOIUrl":"10.1016/j.lanmic.2025.101196","url":null,"abstract":"<div><h3>Background</h3><div>Parasites are foundational to ecosystem health both as indicator species of community productivity and as drivers of diversity. In bacterial communities, bacteriophage viruses can have such roles as they track and modulate the dynamic composition of bacterial hosts within an ecosystem. We aimed to test whether viromes can be used as broad signatures of microbiome health using previously published results across systems.</div></div><div><h3>Methods</h3><div>In this systematic review and meta-analysis, we searched PubMed, Google Scholar, Scopus, and Web of Science from Jan 22, 2022, to Sept 17, 2024, for peer-reviewed, primary literature published in English, using search terms “phage diversity”, “microbiome”, “virome”, “virus”, “phageome”, “disease”, and “dysbiosis”. Inclusion criteria were: a comparison between a dysbiosis state and a healthy state in a human or animal host; a defined host organism and microbiome site; examination of the virome; an obtained measure of virome diversity (α, β, or both); use of statistical analysis to assess whether α or β diversity are changed in dysbiosis; and sufficient methodology description on viral isolation and on virus sequence analysis pipeline. We conducted a qualitative data analysis to assess factors explaining changes to virome diversity in dysbiosis. We then calculated response ratios for each study to test for overall patterns of virome α diversity change under disturbance. Finally, we conducted a quantitative analysis on studies from which we were able to obtain paired virome and bacteriome α diversity data to examine the correlation between these data in defined health compared with defined disturbance conditions. This study was not registered.</div></div><div><h3>Findings</h3><div>We identified a total of 74 studies for inclusion that spanned human (n=61), mouse (n=8), pig (n=3), dog (n=1), and cow (n=1) hosts and a diverse spectrum of infections and diseases. By comparing observed phage and bacterial diversity in microbiomes characterised by dysbiosis with those considered control populations, we were able to identify some key commonalities. Of the 69 studies that investigated changes to α diversity of the virome in dysbiosis, 28 (41%) reported significant changes, but with variable directional change. Of 38 datasets (from 30 studies) for which virome α diversity values were available, 22 (58%) gave a response ratio of less than 1 (α diversity decreases in dysbiosis) and 16 (42%) of more than 1 (α diversity increases in dysbiosis); however, in 27 (71%) datasets, 95% CIs overlapped with 1 (ie, no change in α diversity). We found shifting virome composition to be a more consistent signature of dysbiosis, with 47 (69%) of 68 studies reporting a significant change in viral β diversity with dysbiosis. 62 (89%) of 70 studies reported significant enrichment of system-specific viral taxa under dysbiosis. Our quantitative correlation analysis suggested that bacterial α diversi","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101196"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281376","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101200
Chao Yan MD , Shanwei Tong MS , Yarong Wu PhD , Yujie Chen MBBS , Xinyu Jia MBBS , Yan Guo PhD , Mengnan Cui MS , Guangqian Pei MS , Zuming Zhang BSc , Hao Zhou BAdmin , Kai Mu MS , Xue Ren MS , Bing Du MS , Hanqing Zhao MBBS , Yanling Feng MBBS , Jinghua Cui MD , Yuyan Xia MBBS , Zhen Wang MS , Yu Sun MS , Prof Linqing Zhao MD , Prof Yujun Cui PhD
Background
After a prolonged period of low detection rates, Mycoplasma pneumoniae resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen.
Methods
We sequenced 685 M pneumoniae isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013–22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen’s evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China.
Findings
Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China’s large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China.
Interpretation
Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen.
Funding
National Key Research and Development Program of China, National Natural Science Foundation of China for Key Programs of China Grants, and Beijing High-Level Public Health Technical Talent Project.
{"title":"Macrolide-resistant Mycoplasma pneumoniae resurgence in Chinese children in 2023: a longitudinal, cross-sectional, genomic epidemiology study","authors":"Chao Yan MD , Shanwei Tong MS , Yarong Wu PhD , Yujie Chen MBBS , Xinyu Jia MBBS , Yan Guo PhD , Mengnan Cui MS , Guangqian Pei MS , Zuming Zhang BSc , Hao Zhou BAdmin , Kai Mu MS , Xue Ren MS , Bing Du MS , Hanqing Zhao MBBS , Yanling Feng MBBS , Jinghua Cui MD , Yuyan Xia MBBS , Zhen Wang MS , Yu Sun MS , Prof Linqing Zhao MD , Prof Yujun Cui PhD","doi":"10.1016/j.lanmic.2025.101200","DOIUrl":"10.1016/j.lanmic.2025.101200","url":null,"abstract":"<div><h3>Background</h3><div>After a prolonged period of low detection rates, <em>Mycoplasma pneumoniae</em> resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen.</div></div><div><h3>Methods</h3><div>We sequenced 685 <em>M pneumoniae</em> isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013–22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen’s evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China.</div></div><div><h3>Findings</h3><div>Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China’s large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China.</div></div><div><h3>Interpretation</h3><div>Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen.</div></div><div><h3>Funding</h3><div>National Key Research and Development Program of China, National Natural Science Foundation of China for Key Programs of China Grants, and Beijing High-Level Public Health Technical Talent Project.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101200"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145655792","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}
Pub Date : 2025-12-01DOI: 10.1016/j.lanmic.2025.101306
The Lancet Microbe
{"title":"Neglected tropical diseases: golden age of elimination?","authors":"The Lancet Microbe","doi":"10.1016/j.lanmic.2025.101306","DOIUrl":"10.1016/j.lanmic.2025.101306","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 12","pages":"Article 101306"},"PeriodicalIF":20.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145655843","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}
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