Microbial Genomics最新文献

{"title":"Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 <i>Vibrio cholerae</i> in foodborne outbreaks.","authors":"Masatomo Morita, Hirotaka Hiyoshi, Eiji Arakawa, Hidemasa Izumiya, Makoto Ohnishi, Kikuyo Ogata, Mari Sasaki, Hiroshi Narimatsu, Emiko Kitagawa, Yukihiro Akeda, Toshio Kodama","doi":"10.1099/mgen.0.001364","DOIUrl":"10.1099/mgen.0.001364","url":null,"abstract":"<p><p>In 2013, foodborne outbreaks in Japan were linked to non-O1, non-O139 <i>Vibrio cholerae</i>. However, laboratory tests have detected several serogroups, making it difficult to determine the causative agent. Therefore, whole-genome analyses revealed that only serogroup O144 <i>V. cholerae</i> possesses a genomic island with a type III secretion system (T3SS). A T3SS-deficient mutant was subsequently generated, and its pathogenicity was assessed using a rabbit ileal loop test. This led to the conclusion that serogroup O144 <i>V. cholerae</i> with T3SS was the causative agent of foodborne outbreaks. This study provides an illustrative example of the utilization of whole-genome data for pathogenicity and molecular epidemiological analyses in outbreak investigations.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11865499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516114","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 of <i>Acinetobacter baumannii</i> clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020), revealed the predominance of the Global Clone 2 lineage.","authors":"Nurul Saidah Din, Farahiyah Mohd Rani, Ahmed Ghazi Alattraqchi, Salwani Ismail, Nor Iza A Rahman, David W Cleary, Stuart C Clarke, Chew Chieng Yeo","doi":"10.1099/mgen.0.001345","DOIUrl":"10.1099/mgen.0.001345","url":null,"abstract":"<p><p>Carbapenem-resistant <i>Acinetobacter baumannii</i> is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 <i>A</i>. <i>baumannii</i> isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011-2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (<i>n</i>=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu <i>A. baumannii</i> clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2_Pasteur of the Global Clone 2 lineage identified as the dominant ST (<i>n</i>=76/126; 60.3%). The ST2_Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195_Oxford (<i>n</i>=35) and ST208_Oxford (<i>n</i>=17). Various antimicrobial resistance genes were identified with the <i>bla</i> _OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (<i>n</i>=90/126; 71.4%). Plasmid-encoded <i>rep</i> genes were identified in nearly all (<i>n</i>=122/126; 96.8%) of the isolates with the majority being Rep_3 family (<i>n</i>=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2_Pasteur isolates harbouring them. This study provided a genomic snapshot of the <i>A. baumannii</i> isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2_Pasteur lineage, indicating the entrenchment of this clone in the hospital.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189807","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 insights into the beneficial potential of <i>Bifidobacterium</i> and <i>Enterococcus</i> strains isolated from Cameroonian infants.","authors":"Pierre Marie Kaktcham, Magdalena Kujawska, Edith Marius Foko Kouam, Laverdure Tchamani Piame, Michele Letitia Tchabou Tientcheu, Julia Mueller, Angela Felsl, Bastian-Alexander Truppel, François Zambou Ngoufack, Lindsay J Hall","doi":"10.1099/mgen.0.001354","DOIUrl":"10.1099/mgen.0.001354","url":null,"abstract":"<p><p>A healthy early-life gut microbiota plays an important role in maintaining immediate and long-term health. Perturbations, particularly in low- to middle-income communities, are associated with increased infection risk. Thus, a promising avenue for restoring a healthy infant microbiota is to select key beneficial bacterial candidates from underexplored microbiomes for developing new probiotic-based therapies. This study aimed to recover bifidobacteria and lactic acid bacteria from the faeces of healthy Cameroonian infants and unravel the genetic basis of their beneficial properties. Faecal samples were collected from 26 infants aged 0-5 months recruited in Dschang (Cameroon). Recovered bacterial isolates were subjected to whole-genome sequencing and <i>in silico</i> analysis to assess their potential for carbohydrate utilization, their antimicrobial capacities, host-adaptation capabilities and their safety. From the range of infant-associated <i>Bifidobacterium</i> and <i>Enterococcus</i> strains identified, <i>Bifidobacterium</i> species were found to harbour putative gene clusters implicated in human milk oligosaccharide metabolism. Genes linked to the production of antimicrobial peptides such as class IV lanthipeptides were found in <i>Bifidobacterium pseudocatenulatum</i>, while those implicated in biosynthesis of cytolysins, enterolysins, enterocins and propeptins, among others, were identified in enterococci. Bifidobacterial isolates did not contain genes associated with virulence; however, we detected the presence of putative tetracycline resistance genes in several strains belonging to <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> and <i>Bifidobacterium longum</i> subsp. <i>longum</i>. Among the enterococci, <i>Enterococcus mundtii</i> PM10 did not carry any genes associated with antimicrobial resistance or virulence. The latter, together with all the <i>Bifidobacterium</i> strains, also encoded several putative adaptive and stress-response-related genes, suggesting robust gastroinstestinal tract colonization potential. This work provides the first genomic characterization of <i>Bifidobacterium</i> and <i>Enterococcus</i> isolates from Cameroonian infants. Several strains showed the genomic potential to confer beneficial properties. Further phenotypic and clinical investigations are needed to confirm their suitability as customized probiotics.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448573","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":"Evaluating methods for genome sequencing of <i>Chlamydia trachomatis</i> and other sexually transmitted bacteria directly from clinical swabs.","authors":"Karina Andrea Büttner, Vera Bregy, Fanny Wegner, Srinithi Purushothaman, Frank Imkamp, Tim Roloff Handschin, Mirja H Puolakkainen, Eija Hiltunen-Back, Domnique Braun, Ibrahim Kisakesen, Andreas Schreiber, Andrea Carolina Entrocassi, María Lucía Gallo Vaulet, Deysi López Aquino, Laura Svidler López, Luciana La Rosa, Adrian Egli, Marcelo Rodríguez Fermepin, Helena Mb Seth-Smith, On Behalf Of The Escmid Study Group For Mycoplasma And Chlamydia Infections Esgmac","doi":"10.1099/mgen.0.001353","DOIUrl":"https://doi.org/10.1099/mgen.0.001353","url":null,"abstract":"<p><p>Rates of bacterial sexually transmitted infections (STIs) are rising, and accessing their genomes provides information on strain evolution, circulating strains and encoded antimicrobial resistance (AMR). Notable pathogens include <i>Chlamydia trachomatis</i> (CT), <i>Neisseria gonorrhoeae</i> (NG) and <i>Treponema pallidum</i> (TP), globally the most common bacterial STIs. <i>Mycoplasmoides</i> (formerly <i>Mycoplasma</i>) <i>genitalium</i> (MG) is also a bacterial STI that is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole-genome sequences and evaluated four approaches using clinical samples from Argentina (39), and Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low-load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies, which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT-positive samples, from 36% of NG-positive samples and 60% of TP-positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. These data can be utilized to examine circulating strains and genotypic resistance and guide public health strategies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409050","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":"The complete genome sequence of <i>Penaeus vannamei</i> nudivirus (previously Baculovirus penaei or <i>P. vannamei</i> singly enveloped nuclear polyhedrosis virus).","authors":"Hung N Mai, Arun K Dhar","doi":"10.1099/mgen.0.001360","DOIUrl":"https://doi.org/10.1099/mgen.0.001360","url":null,"abstract":"<p><p><i>Penaeus vannamei</i> singly enveloped nuclear polyhedrosis virus (PvSNPV), also known as Baculovirus penaei (BP), is the first viral pathogen of penaeid shrimp described in 1974. Although PvSNPV was discovered almost 50 years ago, the complete genome sequence has not been elucidated until now. We detected the virus in a quarantine stock of <i>P. vannamei</i> shrimp by light microscopy of faecal samples and by PCR screening of broodstock. Subsequently, next-generation sequencing was deployed to determine the complete genome sequence of PvSNPV. The PvSNPV genome is a circular, double-stranded DNA molecule of 119 883 bp in length encoding 101 ORFs. The deduced aa sequences from 28 ORFs were homologous to 28 core proteins from all identified nudiviruses. Phylogenetic analyses based on deduced aa sequences of the core genes and orthologous genes revealed that PvSNPV clusters with <i>Penaeus monodon</i> nudivirus. Therefore, we propose to rename BP/PvSNPV as <i>P. vannamei</i> nudivirus and re-assign the virus to the family <i>Nudiviridae</i> instead of <i>Baculoviridae</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516118","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":"Molecular epidemiology of <i>Eimeria</i> spp. parasites and the faecal microbiome of Indiana bats (<i>Myotis sodalis</i>): a non-invasive, multiplex metabarcode survey of an endangered species.","authors":"Andrew J Bennett, Cory D Suski, Joy M O'Keefe","doi":"10.1099/mgen.0.001358","DOIUrl":"https://doi.org/10.1099/mgen.0.001358","url":null,"abstract":"<p><p>Assessing individual and population health in endangered wildlife poses unique challenges due to the lack of an adequate baseline and ethical constraints on invasive sampling. For endangered bats, minimally invasive samples like guano can often be the ethical and technical limit for studies of pathogens and the microbiome. In this study, we use multiplex metabarcode sequencing to describe the faecal microbiome and parasites of 56 Indiana bats (<i>Myotis sodalis</i>). We show evidence of a high prevalence of <i>Eimeria</i> spp. protozoan parasite and characterize associations between infection and changes to the faecal microbiome. We identify a strong and significant enrichment of <i>Clostridium</i> species in <i>Eimeria</i>-positive bats, including isolates related to <i>Clostridium perfringens</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516116","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":"Exploring SNP filtering strategies: the influence of strict vs soft core.","authors":"Mona L Taouk, Leo A Featherstone, George Taiaroa, Torsten Seemann, Danielle J Ingle, Timothy P Stinear, Ryan R Wick","doi":"10.1099/mgen.0.001346","DOIUrl":"10.1099/mgen.0.001346","url":null,"abstract":"<p><p>Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample. However, as sample size and genome diversity increase, a strict core can shrink markedly, discarding potentially informative data. Here, we propose and provide evidence to support the use of a 'soft core' that tolerates some missing data, preserving more information for phylogenetic analysis. Using large datasets of <i>Neisseria gonorrhoeae</i> and <i>Salmonella enterica</i> serovar Typhi, we assess different core thresholds. Our results show that strict cores can drastically reduce informative sites compared to soft cores. In a 10 000-genome alignment of <i>Salmonella enterica</i> serovar Typhi, a 95% soft core yielded ten times more informative sites than a 100% strict core. Similar patterns were observed in <i>N. gonorrhoeae</i>. We further evaluated the accuracy of phylogenies built from strict- and soft-core alignments using datasets with strong temporal signals. Soft-core alignments generally outperformed strict cores in producing trees displaying clock-like behaviour; for instance, the <i>N. gonorrhoeae</i> 95% soft-core phylogeny had a root-to-tip regression <i>R</i> ² of 0.50 compared to 0.21 for the strict-core phylogeny. This study suggests that soft-core strategies are preferable for large, diverse microbial datasets. To facilitate this, we developed <i>Core-SNP-filter</i> (https://github.com/rrwick/Core-SNP-filter), an open-source software tool for generating soft-core alignments from whole-genome alignments based on user-defined thresholds.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984006","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":"<i>Clostridioides difficile</i> recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences.","authors":"Emmanuel O Ngbede, Vera Junker, Baban Kolte, Martinique Frentrup, Judith Boldt, Warren N Fawley, Mark H Wilcox, Ed J Kuijper, Wiep Klaas Smits, Ulrich Nübel","doi":"10.1099/mgen.0.001342","DOIUrl":"https://doi.org/10.1099/mgen.0.001342","url":null,"abstract":"<p><p>Genomic data on <i>Clostridioides difficile</i> from the African continent are currently lacking, resulting in the region being under-represented in global analyses of <i>C. difficile</i> infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare <i>C. difficile</i> isolates from diarrhoeic human patients (<i>n</i>=142), livestock (<i>n</i>=38), poultry manure (<i>n</i>=5) and dogs (<i>n</i>=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global <i>C. difficile</i> population. In addition, selected isolates were tested for antimicrobial susceptibility (<i>n</i>=33) and characterized by PCR ribotyping (<i>n</i>=53). Hierarchical clustering of core-genome multilocus sequence typing (cgMLST) allelic profiles revealed large diversity at the level HC150 (i.e. clusters of related genomes with maximally 150 pairwise allelic differences), which was previously shown to correlate with PCR ribotypes (RT). While several globally disseminated strains were detected, including HC150_1 (associated with RT078), HC150_3 (RT001) and HC150_3622 (RT014), 42 HC150 clusters (79%) represented unique genotypes that were new to the public genomic record, and 16 (30%) of these were novel PCR ribotypes. Considerable proportions of the <i>C. difficile</i> isolates displayed resistance to fluoroquinolones, macrolides and linezolid, potentially reflecting human and animal antibiotic consumption patterns in the region. Notably, our comparative phylogenomic analyses revealed human-human, human-livestock and farm-farm sharing of near-identical <i>C. difficile</i> genomes (≤2 core-genome allelic differences), suggesting the continued spread of multiple strains across human and animal (pig, poultry, cattle and dog) host populations. Our findings highlight the interconnectivity between livestock production and the epidemiology of human CDI and inform the need for increased CDI awareness among clinicians in this region. A large proportion of <i>C. difficile</i> strains appeared to be unique to the region, reflecting both the significant geographic patterning present in the <i>C. difficile</i> population and a general need for additional pathogen sequencing data from Africa.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066577","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":"The dominant lineage of an emerging pathogen harbours contact-dependent inhibition systems.","authors":"Cristian V Crisan, Joanna B Goldberg","doi":"10.1099/mgen.0.001332","DOIUrl":"10.1099/mgen.0.001332","url":null,"abstract":"<p><p>Bacteria from the <i>Stenotrophomonas maltophilia</i> complex (Smc) are important multidrug-resistant pathogens that cause a broad range of infections. Smc is genomically diverse and has been classified into 23 lineages. Lineage Sm6 is the most common among sequenced strains, but it is unclear why this lineage has evolved to be dominant. Antagonistic interactions can significantly affect the evolution of bacterial populations. These interactions may be mediated by secreted contact-dependent proteins, which allow inhibitor cells to intoxicate adjacent target bacteria. Contact-dependent inhibition (CDI) requires three proteins: CdiA, CdiB and CdiI. CdiA is a large, filamentous protein exported to the surface of inhibitor cells through the pore-like CdiB. The CdiA C-terminal domain (CdiA-CT) is toxic when delivered into target cells of the same species or genus. CdiI immunity proteins neutralize the toxicity of cognate CdiA-CT toxins. We found that all complete Smc genomes from the Sm6 lineage harbour at least one CDI locus. By contrast, less than a quarter of strains from other lineages have CDI genes. Smc CdiA-CT domains are diverse and have a broad range of predicted functions. Most Sm6 strains harbour non-cognate <i>cdiI</i> genes predicted to provide protection against foreign toxins from other strains. Finally, we demonstrated that an Smc CdiA-CT toxin has antibacterial properties and is neutralized by its cognate CdiI.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11893273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033497","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":"Diversification of <i>bla</i> _OXA-48-harbouring plasmids among carbapenemase-producing <i>Enterobacterales</i>, 11 years after a large outbreak in a general hospital in the Netherlands.","authors":"Pieter W Smit, Carla van Tienen, Fabian Landman, Sabrina Zagers, Marije den Drijver, Arjan Burggraaf, Daan W Notermans, Marjolein Damen, Antoni P A Hendrickx, Casper Jamin","doi":"10.1099/mgen.0.001335","DOIUrl":"10.1099/mgen.0.001335","url":null,"abstract":"<p><p><b>Introduction.</b> Genes encoding OXA-48-like carbapenem-hydrolyzing enzymes are often located on plasmids and are abundant among carbapenemase-producing <i>Enterobacterales</i> (CPE) worldwide. After a large <i>bla</i> _OXA-48 plasmid-mediated outbreak in 2011, routine screening of patients at risk of CPE carriage on admission and every 7 days during hospitalization was implemented in a large hospital in the Netherlands. The objective of this study was to investigate the dynamics of the hospitals' 2011 outbreak-associated <i>bla</i> _OXA-48 plasmid among CPE collected from 2011 to 2021.<b>Methods.</b> A selection of 86 <i>bla</i> _OXA-48-carrying CPE isolates was made from 374 isolates collected over an 11-year study period. Species included <i>Escherichia coli</i> (Eco), <i>Klebsiella pneumoniae</i> (Kpn), <i>Enterobacter cloacae complex</i> (Ecl), <i>Citrobacter freundii</i> (Cfr), <i>Citrobacter koseri</i> (Cko) and <i>Morganella morgani</i> (Mmo). Short-read sequencing was combined with long-read sequencing for all isolates to reconstruct <i>bla</i> _OXA-48-like plasmids and chromosomes of CPE. MASH, MOBsuite, ResFinder, PlasmidFinder and SNP analyses were performed to study diversity. pOXA-48 plasmids were compared to plasmid sequences that were sequenced for the Dutch CPE surveillance in the same time period.<b>Results.</b> In total for the 86 CPE, 2 failed genomic assemblies and 78 <i>bla</i> _OXA-48-encoding plasmids were reconstructed, and six <i>bla</i> _OXA-48 genes were located chromosomally. The 2011 outbreak-associated <i>bla</i> _OXA-48 plasmid of 63.6 kb with IncL replicon was found in Cfr, Ecl, Eco, Kpn and Mmo and primarily between 2011 and 2014 and indicated as LR025105 as MASH nearest neighbour. From 2014 onwards, 11 other types of <i>bla</i> _OXA-48-carrying plasmids with different antibiotic-resistant genes and replicons were discovered, representing the earlier defined distinct pOXA-48 plasmid groups found in the Netherlands. Furthermore, on a national level, the LR025105 plasmid was found after 2015 in many different bacterial backgrounds, highlighting the promiscuous nature of this pOXA-48 plasmid.<b>Conclusion.</b> After a large <i>bla</i> _OXA-48 outbreak in a large hospital in the Netherlands, the composition of the <i>bla</i> _OXA-48 plasmid population in this hospital diversified over time and is in line with national surveillance data. Plasmid sequencing provided valuable insight into the transmission dynamics of <i>bla</i> _OXA-48-encoding plasmids and showed no indication of the persistence of the 2011 <i>bla</i> _OXA-48 plasmid in the hospital environment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951318","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}