Microbial Genomics最新文献

{"title":"Evidence supporting the first secondary chromosome in Actinobacteria as a hallmark of the <i>Embleya</i> genus.","authors":"Juan Pablo Gomez-Escribano, Siobhán Dorai-Raj, David Baker, Ernest Lacey, Barrie Wilkinson, Thomas J Booth","doi":"10.1099/mgen.0.001704","DOIUrl":"10.1099/mgen.0.001704","url":null,"abstract":"<p><p><i>Embleya</i> is a genus within the family <i>Streptomycetaceae</i>, a group of Actinobacteria with an outstanding capacity for the production of specialized metabolites, and a strikingly complex life cycle. In this work, we sequenced the complete genome of the new species <i>Embleya australiensis</i> MST-111070 and validated the assembly using optical mapping. The genome of <i>E. australiensis</i> MST-111070 consists of a 7.1 Mb linear chromosome and three additional replicons (EEC, <i>Embleya</i> extrachromosomal element), including a 4.2 Mb linear replicon, EEC1, significantly larger than all previously described secondary replicons from bacteria. EEC1 is typified by its similar composition to the chromosome in terms of G+C content, codon usage and gene functions. It also carries terminal inverted repeats identical to the chromosome. EEC1 is enriched in biosynthetic gene clusters (BGCs), including the only copy of the BGCs for the spore pigment and the surfactant peptide SapB, metabolites essential for the organism's life cycle. EEC1 contains an origin of replication with at least some chromosomal properties, and its replication is likely to depend on functions provided by chromosomally located genes. Further comparison of <i>Embleya</i> spp. genomes suggests that EEC1-like replicons are conserved across the genus, in contrast to other known large linear extrachromosomal replicons (megaplasmids) in the family <i>Streptomycetaceae</i>. EEC1 is thus a hallmark of the <i>Embleya</i> genus and is central to its evolution within the <i>Streptomycetaceae</i> family. We propose EEC1 as a secondary chromosome and the largest secondary replicon reported in bacteria to date.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13152386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome sequencing to investigate the prevalence and transmission of multidrug-resistant Gram-negative pathogens in an adult intensive care unit in the UK.","authors":"Hayley J Wilson, Petra Polgarova, Fahad A Khokhar, Ben Warne, Rory Carpenter, Beth Blane, David A Enoch, Nicholas M Brown, Jacobus Preller, Charlotte Summers, Sharon J Peacock, Gordon Dougan, Julian Parkhill, Nicholas R Thomson, Mili Estée Török","doi":"10.1099/mgen.0.001654","DOIUrl":"https://doi.org/10.1099/mgen.0.001654","url":null,"abstract":"<p><p><b>Background.</b> Rates of multidrug resistance (MDR) in Gram-negative bacteria (GNB), particularly those harbouring extended-spectrum beta-lactamases (ESBL) and/or carbapenemases, are increasing globally. Intensive care unit (ICU) patients are vulnerable to healthcare-associated infection (HCAI). Surveillance for carriage of multidrug-resistant Gram-negative bacteria (MDR GNB) is inconsistent, with differing practices amongst ICUs, hospitals and countries. Furthermore, the impact of asymptomatic carriage on HCAI rates is unclear.<b>Methods.</b> We conducted a 6-month prospective surveillance study of MDR GNB in a UK adult ICU. Screening samples were collected from all study participants on admission, once a week (depending on length of stay) and on discharge from the ICU. Whole-genome sequencing (WGS) was used to examine the population structure and antimicrobial resistance mechanisms of MDR GNB and to determine evidence of recent transmission between patients.<b>Findings.</b> Of 424 participants recruited between June and December 2016, 15% (<i>n</i>=64) were positive for MDR GNB during admission screening to the ICU. The most frequently identified organisms were <i>Pseudomonas aeruginosa</i>, <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i>. In total, 10% (<i>n</i>=42) of patients acquired an ESBL-producing or carbapenem-resistant MDR GNB during their ICU admission. WGS of the bacterial populations reflected national trends. An undetected outbreak of carbapenemase-producing <i>K. pneumoniae</i>, which had spread to several wards, was identified and controlled. Most positive patients carried identical lineages across multiple body sites.<b>Interpretation.</b> Our findings suggest that prospective screening for MDR GNB in ICU patients could be beneficial and be considered in other UK critical care settings. This would not only improve early detection but also enable the prompt institution of enhanced infection control measures.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics and molecular insights into smooth and rough clinical isolates of <i>Mycobacterium abscessus</i>.","authors":"Rajender Kumar, Clara Braian, Gabrielle Fröberg, Lina Davies Forsman, Thomas Schön","doi":"10.1099/mgen.0.001687","DOIUrl":"https://doi.org/10.1099/mgen.0.001687","url":null,"abstract":"<p><p><b>Background.</b> Our recent findings indicate that the rough form of the <i>Mycobacterium abscessus</i> complex (MABC) is associated with worse clinical outcomes compared to the smooth variant. The glycopeptidolipid (GPL) locus has been considered vital for this transition; however, this has only been shown during <i>in vitro</i> selection. Thus, we aimed to investigate genetic differences between the morphotypes among clinical isolates.<b>Methods.</b> Whole-genome sequencing (WGS) by Oxford Nanopore was applied to rough and smooth clinical MABC strains (<i>n</i>=10), including laboratory strains and <i>in vitro</i> exposure to nitric oxide (NO). Comparative genomic analysis, methylation and pangenome analysis were used to investigate the orthologs and unique protein clusters in relation to morphotype.<b>Results.</b> WGS analysis showed high average nucleotide sequence identity (>98%), but genetic variants compared to the reference genome ranged from 1,433 to 27,025, and these differences did not correlate with morphotype. Among clinical isolates, smooth MABC clustered and were separated from the rough isolates. In both rough and smooth phenotypes, random genetic variations that could not separate the morphotypes were detected mainly in the <i>nrps</i> of the GPL loci. The major protein-cluster differences between smooth (<i>n</i>=123) and rough (<i>n</i>=22) clinical isolates were observed in key genes outside the GPL locus, such as <i>fabH</i>, <i>pks15</i>, <i>fadD29</i>, <i>otaA</i>, <i>mabA</i>, <i>lysX</i> and <i>acdA</i>, primarily involved in fatty acid biosynthesis and transporter systems. Repeated NO exposure, serving as a proxy for host-related stress, induced a rough phenotype by altering the acyl desaturase DesA1 protein, which is involved in fatty acid synthesis.<b>Conclusion.</b> By analysing clinical MABC isolates, we show that morphotype variation cannot be explained by the GPL locus only. Unique genes involved in fatty acid biosynthesis were identified, informing further investigation into mechanisms distinguishing smooth and rough morphotypes of clinical MABC isolates.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Geographic clustering and population structures of <i>Campylobacter jejuni</i> and <i>Campylobacter coli</i> in South and Southeast Asian poultry systems.","authors":"Burhan Lehri, Le Thi Hong Nhung, Keya Ghosh, Tahia Ahmed Logno, Mahamudul Hasan, G Weerasooriya, M A R Priyantha, P S De Alwis, Venkateshprabhu Janagaraj, Zayina Zondervenni Manoharan, Sadiq Dantroliya, Ramesh Pandit, Chaitanya Joshi, Luu Quynh Huong, M Anandachitra, Madhvi Joshi, Rashed Mahmud, Pham Thi Ngoc, Archibald Coombs, Ying Ying Chrystal Li, Mahati Ramachandra, Saira Butt, Samuel M Ronald, Anne Conan, Paritosh Kumar Biswas, Mohammed Abdus Samad, Ruwani Kalupahana, Sitara Swarna Rao Ajjampur, Guillaume Fournie, Brendan W Wren, Fiona Tomley, Damer P Blake, Richard A Stabler","doi":"10.1099/mgen.0.001706","DOIUrl":"10.1099/mgen.0.001706","url":null,"abstract":"<p><p>Poultry production is rapidly expanding across South and Southeast Asia to meet rising demand for human consumption. <i>Campylobacter jejuni</i> and <i>Campylobacter coli</i> are the leading causes of human bacterial gastroenteritis worldwide, with poultry serving as a primary reservoir posing significant risks to food safety and public health. This study investigated the genetic diversity of <i>C. jejuni</i> and <i>C. coli</i> isolates from chicken sampled in farms, along with markets (live bird markets and shops) and slaughtering facilities from Bangladesh, India, Sri Lanka and Vietnam. Core-genome multilocus sequence typing revealed strong geographical clustering of <i>C. coli</i> isolates, dominated by ST-828 clonal complex lineages largely confined within national borders. In contrast, <i>C. jejuni</i> isolates clustered more diffusely into multiple clonal complexes (ST-21, ST-45 and ST-257) that were shared between countries, reflecting greater ecological adaptability and frequent gene flow. Permutational multivariate ANOVA (PERMANOVA) supported these patterns; geography explained more genomic variation for <i>C. coli</i> than <i>C. jejuni,</i> while poultry breed type and production site contributed little overall. An exception was Sri Lanka, where <i>C. jejuni</i> showed an apparent ecological segregation between markets and slaughtering facilities, albeit with a limited within-country sample size. Genomic SNP-based analysis highlighted recombination as a significant evolutionary force maintaining distinct country-specific lineages in <i>C. coli</i>, while supporting a broader geographic mixing of <i>C. jejuni</i>. Pangenome analyses were consistent with more geographically structured accessory profiles in <i>C. coli</i> and a more dispersed pattern in <i>C. jejuni</i>, compatible with broader regional dissemination. Comparison with global reference genomes showed these isolates clustered with strains from diverse host species, highlighting the ability of <i>C. jejuni</i> to occupy multiple ecological niches and spread across borders. The distinct patterns of spatially clustered and dispersed lineage distributions for <i>C. coli</i> and <i>C. jejuni</i>, respectively, highlight the importance of understanding species-specific transmission dynamics to inform targeted intervention strategies. This understanding underscores the need for interventions along poultry production and distribution networks that can effectively mitigate the risks associated with campylobacteriosis.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13152252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of a nosocomial outbreak of ST101 <i>Klebsiella pneumoniae</i> carrying <i>bla</i> _OXA-48 in Shandong, China.","authors":"Wanxiang Li, Qizhao Gao, Jie Ma, Zhichen Zhu, Jie Zhu, Liang Wang, Yicheng Wen, Yaxuan Zhai, Liang Chen, Hong Du","doi":"10.1099/mgen.0.001683","DOIUrl":"https://doi.org/10.1099/mgen.0.001683","url":null,"abstract":"<p><p><b>Objectives</b>. Carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP) strains harbouring <i>bla</i> _KPC and <i>bla</i> _NDM are prevalent in China, while <i>bla</i> _OXA-48-positive CRKP remains uncommon. This study reports one of the first outbreaks of a nosocomial infection caused by ST101 <i>bla</i> _OXA-48-positive CRKP in China.<b>Methods</b>. We conducted a retrospective molecular epidemiological study of 269 CRKP isolates collected at a tertiary hospital in China, between 2012 and 2022. Antimicrobial susceptibility testing, whole-genome sequencing, phylogenetic analyses and plasmid characterization were performed to investigate the clinical and molecular features of <i>bla</i> _OXA-48-CRKP. Conjugation assays were used to assess plasmid transferability.<b>Results</b>. Among the 269 CRKP isolates, we identified 61 <i>bla</i> _OXA-48-positive strains from 38 patients. Most cases were linked to the intensive care unit (ICU), with patient transfers facilitating spread to non-ICU wards and branch hospitals. The outbreak was associated with a high mortality rate (63.2%), including 42.1% within 30 days. Genomic analysis revealed that 59 isolates belonged to ST101 and carried multiple resistance determinants. All <i>bla</i> _OXA-48 genes were located on IncL plasmids, which evolved into three structural variants during the outbreak. Notably, the late-emerging Type III plasmid had lost conjugative transferability. Core-genome SNP analysis demonstrated clonal expansion within the hospital, while phylogenetic comparisons indicated the likely introduction of ST101 strains from Europe. Global phylogenomic analysis revealed complex intercontinental transmission pathways, underscoring the lineage's high potential for global dissemination.<b>Conclusions</b>. We documented the first hospital outbreak in China caused by ST101 <i>bla</i> _OXA-48-positive CRKP. This study improves our understanding of plasmid evolution during nosocomial outbreaks and provides valuable insights to guide infection control strategies of plasmid-mediated resistance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic comparison of clinical strains of <i>Mycobacterium shinjukuense</i> in Japan reveals low diversity and stable genome structures.","authors":"Takayuki Wada, Hiharu Inoue, Shiomi Yoshida, Yoshiro Murase, Yuriko Igarashi, Yukari Fukushima, Chie Nakajima, Yasuhiko Suzuki, Satoshi Mitarai","doi":"10.1099/mgen.0.001695","DOIUrl":"https://doi.org/10.1099/mgen.0.001695","url":null,"abstract":"<p><p><i>Mycobacterium shinjukuense</i>, a rare non-tuberculous mycobacterial species closely related to <i>Mycobacterium tuberculosis</i>, remains poorly characterized at the genomic level. To obtain insights into its intraspecies genomic diversity and structure variation, we performed whole-genome sequencing on 18 clinical strains of <i>M. shinjukuense</i> collected from Japan between 2010 and 2017. Phylogenetic analysis revealed limited overall genetic diversity, with several clonal clusters likely representing identical strains. The phylogeny exhibited a largely star-like topology with few single nucleotide variations accumulated over time, suggesting a clonal expansion. Complete genome sequencing of five representative strains revealed high synteny, with no large-scale rearrangements, suggesting stable genomic structures. One strain, MSJ-01, harboured a unique 30 kb insertion region, possibly acquired via horizontal gene transfer. These findings provide insights into the genomic diversity and structure of <i>M. shinjukuense</i>, suggesting both its evolutionary stability and its potential to incorporate foreign DNA. This work expands upon available genomic resources and supports the utility of <i>M. shinjukuense</i> as a model for understanding genome evolution in the <i>M. tuberculosis</i>-associated phylotype lineage.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13143225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>Escherichia coli</i> F plasmidome: an Australian perspective.","authors":"Max L Cummins, Anne E Watt, Celeste M Donato, Amy V Jennison, Torsten Seemann, Erica Donner, Cameron J Reid, Danielle J Ingle, Benjamin P Howden, Steven P Djordjevic, On Behalf Of The Australian Pathogen Genomics One Health Working Group","doi":"10.1099/mgen.0.001669","DOIUrl":"https://doi.org/10.1099/mgen.0.001669","url":null,"abstract":"<p><p>ColV/ColBM and ColIa/<i>senB</i> F virulence plasmids feature prominently in <i>Escherichia coli</i> associated with urinary tract and bloodstream infections globally. Australian-sourced <i>E. coli</i> that carry these plasmids were examined among 5,471 isolates (3,316 sequenced by the APG and AusGEM programmes; 2,155 from public databases) spanning years 1986-2020 from humans (<i>n</i>=2,996/5,471; 54.8%), wild animals (<i>n</i>=870/5,471; 15.9%), livestock (<i>n</i>=649/5,471; 11.9%), companion animals (<i>n</i>=375/5,471; 6.9%), environmental sources (<i>n</i>=292/5,471; 5.3%) and food (<i>n</i>=289/5,471; 5.3%). Putative plasmid reconstruction, assisted by a plasmid database comprising 23,700 complete plasmid sequences, identified 22,534 putative plasmids of which 21,814 (96.8%) represented 547 known plasmid clusters. <i>E. coli</i> harbouring ColV-associated putative plasmids, particularly plasmid cluster AA176 [F replicon sequence type (RST): F18:A-:B1 (repFII-18:repFIA-null:repFIB-1)] was identified among phylogenetically diverse strains from humans, livestock, particularly poultry, and food. Closely related isolates, defined as ≤10 core-genome multilocus sequence type allelic distance, that carried either ColV or ColIa/<i>senB</i>-associated putative (F) plasmids were identified across multiple sources and diverse phylogenetic backgrounds. ColIa/<i>senB</i>-associated putative (F) plasmid clusters AA337 (RST: F29:A-:B10) and AA171 (RST: F2:A1:B20) were associated with phylogenetically closely related isolates from humans, wild animals and companion animals, but their absence in <i>E. coli</i> sourced from food and livestock was notable. <i>E. coli</i> carrying ColV and ColIa/<i>senB</i> plasmids frequently exhibit genotypic multidrug resistance, many with critically important antimicrobial resistance genes, highlighting their role in the evolution of clinically problematic lineages. Our study has important epidemiological considerations for understanding the spread of extraintestinal pathogenic and hybrid <i>E. coli</i> lineages across the One Health spectrum.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic characterization of PBP2 as the primary siderophore recognizer in <i>Actinomycetes</i> and other Gram-positive bacteria.","authors":"Linlong Yu, Guanyue Xiong, Zhiyuan Li","doi":"10.1099/mgen.0.001671","DOIUrl":"https://doi.org/10.1099/mgen.0.001671","url":null,"abstract":"<p><p>Iron is a scarce yet essential nutrient for bacteria. Microbes often acquire iron by secreting siderophores, a diverse group of small molecules that form high-affinity complexes with iron for microbial uptake. Understanding microbial iron interaction networks requires detailed characterization of siderophore recognition specificity. In Gram-positive bacteria, substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver them to ABC transporters for import. However, the SBPs responsible for selective recognition remain poorly characterized, hindering large-scale data mining and network reconstruction. Here, we addressed this knowledge gap by systematically analysing siderophore uptake systems, first in five representative genera and then across a comprehensive dataset of 16,232 Gram-positive bacterial genomes. Through a pipeline integrating genome mining, coevolutionary analysis and structural modelling, we established PBP2 (Peripla_BP_2) subtype SBPs as the primary siderophore recognizer family. We revealed that, unlike the physically clustered systems in Gram-negative bacteria, synthetase and recognizer genes in Gram-positive bacteria are sometimes genomically decoupled, yet display coordinated transcriptional regulation by iron-responsive transcription factors. Our findings underscore key differences between Gram-positive and Gram-negative iron acquisition systems, providing foundational knowledge for large-scale inference of siderophore-mediated microbial interactions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147593178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-based source attribution using a One Health <i>Escherichia coli</i> isolate collection from 2013 to 2023 in Scotland.","authors":"Antonia Chalka, Louise Crozier, Adriana Vallejo-Trujillo, Alison Low, Sean McAteer, Vesa Qarkaxhija, Kate Templeton, Sue C Tongue, Judith Evans, Geoff Foster, Catriona Webster, Thomas Evans, Charis A Marwick, Ahmed Raza, Benjamin J Parcell, Matthew T G Holden, Tom McNeilly, Stephen Fitzgerald, Mairi Mitchell, Nuno Silva, Emily Robertshaw-McFarlane, Scott Hamilton, Beth Wells, Clare Hamilton, Eleanor Watson, David Finlay, Julie Bolland, John Redshaw, David Walker, Jane Heywood, Charlotte King, Craig Baker-Austin, Athina Papadopoulou, Andy Powell, Genever Morgan, Gavin K Paterson, Jacqui McElhiney, David L Gally","doi":"10.1099/mgen.0.001693","DOIUrl":"10.1099/mgen.0.001693","url":null,"abstract":"<p><p>Random forest-based source attribution models were developed from a 'One Health' resource comprising 4,230 high-quality whole-genome assemblies from <i>Escherichia coli</i>. These were isolated from a wide range of sources, predominantly originating in Scotland, including wastewater, livestock, food and clinical infections of humans and dogs. Using these models, we derived a probabilistic assignment of <i>E. coli</i> isolates from food, shellfish and water samples to potential livestock and human sources of contamination. The incorporation of <i>E. coli</i> sequences from wastewater alongside those from human clinical infections enabled us to capture a wide diversity of human strains in our analyses. The sequence types (STs) of isolates from human bacteraemia and urinary tract infection (UTI) were compared with livestock and food isolates. While only 2.3% of the <i>E. coli</i> isolated from food samples in the study were from STs primarily associated with human bacteraemia and UTI, the models found a livestock signal associated with 15% of the human clinical isolates. In the food and private water samples, livestock-human co-attribution of <i>E. coli</i> isolates was common and consistent with routine human exposure to specific subsets of livestock <i>E. coli</i>, potentially a result of selection during food and water processing. Overall, this research demonstrates the potential value of including source attribution models in national surveillance programmes to understand the transmission of <i>E. coli</i> through the agri-food chain and support risk management to protect public health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13094829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergence of outbreak-driving high-risk <i>Pseudomonas aeruginosa</i> lineages in Taiwan: phylogenomic insights into ST292 and the ST235* sublineage.","authors":"Chih-Ming Chen, Hui-Ling Tang, Se-Chin Ke, Yi-Pei Lin, Bo-Han Chen, Ru-Hsiou Teng, Chien-Shun Chiou, Min-Chi Lu, Yi-Chyi Lai","doi":"10.1099/mgen.0.001694","DOIUrl":"https://doi.org/10.1099/mgen.0.001694","url":null,"abstract":"<p><p>The global rise of carbapenem-resistant <i>Pseudomonas aeruginosa</i> (CRPA) poses a significant threat to public health. Through active surveillance conducted between 2021 and 2022, we collected 92 distinct CRPA isolates and identified a clonal shift toward high-risk lineages ST235* and ST292. Whole-genome sequencing and phylogenomic analysis revealed that ST235*, a single-locus variant of epidemic ST235, exhibited broader antimicrobial resistance (AMR) and carried a <i>nalD</i> loss-of-function mutation, resulting in MexAB-OprM overexpression. Two ST235* isolates contained a hybrid resistance cassette with <i>bla</i> _KPC-2 and <i>bla</i> _TEM-1, likely acquired through IS<i>26</i>-mediated transfer from <i>Enterobacter hormaechei</i>. Most ST292 isolates demonstrated an extensively drug-resistant phenotype with a <i>bla</i> _CARB-2-containing cassette and a chromosomally integrated tMexC3D-OprJ efflux system. Additionally, ST244 isolates possessed a <i>bla</i> _VIM-2 cassette embedded within a Tn<i>402</i> transposition module (t<i>niABQR-intI1</i>). Multiple copies of <i>tniABQR-intI1</i> carrying AMR genes were exclusively found in the genomes of ST244, representing a novel mechanism. The genomic plasticity of high-risk CRPA lineages emphasizes their capacity to acquire, amplify and disseminate AMR determinants. To combat the spread of CRPA, genomic surveillance and targeted infection control strategies are urgently required.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}