Microbial Genomics最新文献

{"title":"Genomic insights into host<i>-Endozoicomonadaceae</i> cophylogeny.","authors":"Zhuang Shao, Jian Zhang, Jiaxin Li, Jie Li","doi":"10.1099/mgen.0.001384","DOIUrl":"10.1099/mgen.0.001384","url":null,"abstract":"<p><p>The congruence between host and symbiont phylogenies reflects the evolutionary links among ecologically important interactions. As potential key symbionts, the members affiliated to the family <i>Endozoicomonadaceae</i> have previously been investigated for the cophylogenetic relationship with their hosts using their 16S rRNA gene sequences. However, this approach neglects the genomic features of symbionts that may influence the long-term associations between <i>Endozoicomonadaceae</i> members and their hosts. Here, we collected available high-quality genomes of <i>Endozoicomonadaceae</i> from diverse hosts and investigated their genomic features, including genome size, phages, insertion elements and the composition of functional genes. We also tested the host<i>-Endozoicomonadaceae</i> cophylogeny and examined the correlation between the cophylogenetic squared residuals and the genomic features of <i>Endozoicomonadaceae</i> members. Our results revealed a cophylogenetic pattern between members of the <i>Endozoicomonadaceae</i> family and their various hosts. Moreover, we found that the investigated genomes of <i>Endozoicomonadaceae</i> members were differentially eroded by phages and insertion elements. Additionally, <i>Endozoicomonadaceae</i> members with smaller, more eroded genomes tended to exhibit lower cophylogenetic residuals with their hosts. Gene function analysis further revealed that <i>Endozoicomonadaceae</i> members with closer associations with their hosts carried specific genes related to infection processes and host-symbiont interactions. This study suggests that the genomic features of <i>Endozoicomonadaceae</i> members may influence long-term host<i>-Endozoicomonadaceae</i> intimate associations.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772690","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-based characterization of <i>Escherichia albertii</i> strains isolated from paediatric diarrhoeal cases in Kolkata, India.","authors":"Goutam Chowdhury, Yuki Hoshiko, Miki Okuno, Kei Kitahara, M John Albert, Shin-Ichi Miyoshi, Yoshitoshi Ogura, Shanta Dutta, Thandavarayan Ramamurthy, Asish K Mukhopadhyay","doi":"10.1099/mgen.0.001363","DOIUrl":"10.1099/mgen.0.001363","url":null,"abstract":"<p><p><i>Escherichia albertii</i> is a Gram-negative facultative anaerobic bacterium that causes diarrhoea in humans. This study shows the isolation of <i>E. albertii</i> from hospitalized paediatric diarrhoeal cases and genome-based characteristics with putative virulence factors and antimicrobial resistance. <i>E. albertii</i> isolates were identified by species-specific PCR, targeting the gene encoding cytolethal distending toxin (<i>Ea-cdt</i>). The genome of <i>E. albertii</i> was sequenced to identify (i) genes encoding virulence factors (ii) antibiotic resistance-encoding genes, including the mobile genetic elements and (iii) core gene-based phylogenetic relationships and pan-genome features. A total of 10 (1.2%) <i>E. albertii</i> isolates were isolated from 854 faecal samples, of which 6 (60%) were found as the sole pathogen and the remaining 4 (40%) were identified along with other pathogens, such as enteroaggregative <i>Escherichia coli</i>, rotavirus and adenovirus. Patients from whom <i>E. albertii</i> was isolated presented cholera-like diarrhoea, i.e. with watery stool (60%) with moderate dehydration (100%), fever (20%) and abdominal pain (20%). The antimicrobial susceptibility testing of <i>E. albertii</i> showed that most of the isolates were susceptible or reduced susceptible to most of the antibiotics except resistance to erythromycin (80%), tetracycline (50%), nalidixic acid (40%), ampicillin (40%), doxycycline (30%) and ceftriaxone (20%). In the whole-genome sequence, <i>E. albertii</i> isolates revealed several virulence-encoding genes, namely the intimin (<i>eae</i>, <i>E. coli</i> attaching and effacing), the cytolethal distending toxin type II subunit A (<i>cdt-IIA</i>), adhesion (<i>paa</i>, porcine attaching- and effacing-associated), non-LEE (locus of enterocyte effacement) encoded effector A (<i>nleA</i>) and antimicrobial resistance genes (ARGs) conferring resistance to tetracycline (<i>tetA</i>, <i>tetR</i>), sulphonamides (<i>sul2</i>), fluoroquinolones (<i>qnrS</i>) and beta-lactamases (<i>bla</i> _CTX-M, <i>bl</i>a_TEM). The SNP-based phylogenetic analysis of 647 whole genomes of <i>E. albertii</i> isolates from the National Center for Biotechnology Information databases did not reveal any comparable clustering pattern based on the biological source and place of isolation. The genome of some of the <i>E. albertii</i> was closely related to those of the isolates from China and the United Kingdom. The PFGE patterns revealed that most of the <i>E. albertii</i> isolates were distinct clones. This study reports on the extensive genome analysis of diarrhoea-associated <i>E. albertii</i> harbouring multiple virulence and ARGs.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803662","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":"MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers.","authors":"Mohammad Saiful Islam Sajib, Katarina Oravcova, Kirstyn Brunker, Paul Everest, Ma Jowina H Galarion, Manuel Fuentes, Catherine Wilson, Michael E Murphy, Taya Forde","doi":"10.1099/mgen.0.001383","DOIUrl":"10.1099/mgen.0.001383","url":null,"abstract":"<p><p>Bloodstream infections (BSIs) represent a significant global health challenge, and traditional diagnostic methods are suboptimal for timely guiding targeted antibiotic therapy. We introduce MultiSeq-AMR, a rapid and modular nanopore amplicon-sequencing workflow to identify bacterial and fungal species and a comprehensive set of antimicrobial resistance (AMR) genes (<i>n</i>=91) from various types of infection sources. We initially benchmarked MultiSeq-AMR using DNA from 16 bacterial and 5 fungal reference strains and accurately identified all species. AMR gene identification exhibited 99.4% categorical agreement (CA: 153/154 prediction) with whole-genome sequencing. Further validation with 33 BACT/ALERT positive samples from suspected BSI cases revealed 100% accuracy for genus and 96.7% for species identification, with 97.4% CA (151/155) for AMR gene prediction. To accelerate microbiological diagnosis, a 6 h culture enrichment step was tested with MultiSeq-AMR using 15 clinically important bacterial species. Of 13 species selected for sequencing, 11 were correctly identified, with 96% CA (59/61 predictions) for AMR gene identification. With only 2 Mbp yield, sequencing identified 93.7% of species and 89.8% AMR genes initially detected with 20-50 Mbp yield/sample. MultiSeq-AMR holds promise for BSI diagnosis, as species/AMR genes could be identified under 5 h of BACT/ALERT positivity and potentially <11 h of sample collection (rapid-enrichment) for a large set of bacterial species. MultiSeq-AMR gene targets can be modified/increased indefinitely to suit user needs. Further research is required to clinically validate MultiSeq-AMR, especially the rapid enrichment method, to assess its utility in a medical setup and in improving patient outcomes in BSI.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772692","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 the microbial communities in coastal cenote and their hidden biotechnological potential.","authors":"Perla A Contreras-de la Rosa, Susana De la Torre-Zavala, Aileen O Connor-Sánchez, Alejandra Prieto-Davó, Elsa B Góngora-Castillo","doi":"10.1099/mgen.0.001382","DOIUrl":"10.1099/mgen.0.001382","url":null,"abstract":"<p><p>Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772749","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":"Rapid, reference-free identification of bacterial pathogen transmission using optimized split <i>k</i>-mer analysis.","authors":"Christopher H Connor, Charlie K Higgs, Kristy Horan, Jason C Kwong, M Lindsay Grayson, Benjamin P Howden, Torsten Seemann, Claire L Gorrie, Norelle L Sherry","doi":"10.1099/mgen.0.001347","DOIUrl":"10.1099/mgen.0.001347","url":null,"abstract":"<p><p>Infections caused by multidrug-resistant organisms (MDROs) are difficult to treat and often life threatening and place a burden on the healthcare system. Minimizing the transmission of MDROs in hospitals is a global priority with genomics proving to be a powerful tool for identifying the transmission of MDROs. To optimize the utility of genomics for prospective infection control surveillance, results must be available in real time, reproducible and simple to communicate to clinicians. Traditional reference-based approaches suffer from several limitations for prospective genomic surveillance. Whilst reference-free or pairwise genome comparisons avoid some of these limitations, they can be computationally intensive and time consuming. Split <i>k</i>-mer analysis (SKA) offers a viable alternative facilitating rapid reference-free pairwise comparisons of genomic data, but the optimum SKA parameters for the detection of transmission have not been determined. Additionally, the accuracy of SKA-based inferences has not been measured, nor whether modified quality control parameters are required. Here, we explore the performance of 60 SKA parameter combinations across 50 simulations to quantify the false negative and positive SNP proportions for <i>Escherichia coli</i>, <i>Enterococcus faecium</i>, <i>Klebsiella pneumoniae</i> and <i>Staphylococcus aureus</i>. Using the optimum parameter combination, we explore concordance between SKA, multilocus sequence typing (MLST), core genome MLST (cgMLST) and Snippy in a real-world dataset. Lastly, we investigate whether simulated plasmid gain or loss could impact SNP detection with SKA. This work identifies that the use of SKA with sequencing reads, a <i>k</i>-mer length of 19 and a minor allele frequency filter of 0.01 is optimal for MDRO transmission detection. Whilst SNP detection with SKA (when used with sequencing reads) undercalls SNPs compared to Snippy, it is significantly faster, especially with larger datasets. SKA has excellent concordance with MLST and cgMLST and is not impacted by simulated plasmid movement. We propose that the use of SKA for the detection of bacterial pathogen transmission is superior to traditional methodologies, capable of providing results in a much shorter timeframe.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573458","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":"Human respiratory syncytial virus genetic diversity and lineage replacement in Ireland pre- and post-COVID-19 pandemic.","authors":"Alan Rice, Gabriel Gonzalez, Michael Carr, Jonathan Dean, Emer O'Byrne, Lynn Aarts, Harry Vennema, Weronika Banka, Charlene Bennett, Siobhán Cleary, Lisa Domegan, Joan O'Donnell, Maureen O'Leary, Stephanie Goya, Lance Presser, Adam Meijer, Greg Martin, Hirofumi Sawa, Allison Waters, Cillian De Gascun, Daniel Hare","doi":"10.1099/mgen.0.001379","DOIUrl":"10.1099/mgen.0.001379","url":null,"abstract":"<p><p>Human respiratory syncytial virus (HRSV) is a common cause of lower respiratory tract infections globally, and changes in viral epidemiology have been observed in many jurisdictions following the coronavirus disease 2019 (COVID-19) pandemic. Newly licensed vaccines and monoclonal antibodies are anticipated to alleviate the burden on healthcare systems, though such interventions may exert selective pressures on viral evolution. To evaluate the diversity of HRSV in Ireland pre- and post-COVID-19 pandemic, whole-genome sequencing was performed on HRSV-A (<i>n</i>=123) and -B (<i>n</i>=110) samples collected from community and hospitalized cases, during three HRSV seasons between 2021 and 2024. Additionally, G gene sequences, from HRSV-A (<i>n</i>=141) and -B (<i>n</i>=141), collected in the 2015-2019 period were examined. Lineages were assigned by phylogenetic analyses including reference lineages. Phylogenetic trees inferred with the G gene and whole genomes were consistent. Changes in the prevalence of certain lineages post-COVID-19 reflected the impact of non-pharmaceutical interventions (NPIs) introduced to reduce severe acute respiratory syndrome coronavirus 2 transmission, with A.D.1 and A.D.5 the dominant HRSV-A lineages and B.D.E.1 the most prevalent HRSV-B lineage. Similar trends were observed in HRSV lineages circulating across Europe during this time. The emergence of a new lineage was identified as a descendant from A.D.1, with eight distinctive substitutions in proteins G, F and L. Other circulating lineages with aa substitutions were observed in the F glycoprotein, which could impact nirsevimab binding. We provide the first comprehensive analysis of HRSV genomic diversity and evolution in Ireland over the last decade and the impact of the NPIs introduced during the COVID-19 pandemic. This study provides a foundation for future public health surveillance employing pathogen genomics to enable an evidence-based assessment of the impact of pharmaceutical interventions on HRSV evolution and disease severity.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11914048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143649379","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":"Investigating two decades of <i>Streptococcus pneumoniae</i> bacteraemia in the Gelderland area, the Netherlands, using whole-genome sequencing.","authors":"Ana D Sanches Ferreira, Alannah C King, Femke Wolters, Heiman F L Wertheim, Bert Mulder, Caroline M A Swanink, Christa E van der Gaast-de Jongh, Daan W Arends, Nina M van Sorge, Carel Schaars, Harry C H Hung, Paulina A Hawkins, Lesley McGee, Stephen D Bentley, Jan-Willem Veening, Marien I de Jonge, Stephanie W Lo, Amelieke J H Cremers","doi":"10.1099/mgen.0.001377","DOIUrl":"10.1099/mgen.0.001377","url":null,"abstract":"<p><p>In the Netherlands, the 7-valent pneumococcal conjugate vaccine (PCV) was introduced to the childhood immunization programme in 2006 and replaced by the 10-valent PCV (PCV10, GSK) in 2011. To describe invasive pneumococcal disease in the era of childhood PCV vaccination on pneumococcal bacteraemia across all ages, we collected and sequenced 979 pneumococcal blood isolates from consecutive patients with pneumococcal bacteraemia in the Gelderland area, the Netherlands, between 2000 and 2020. In total, 58% of the bacteraemia cases (<i>n</i>=563/979) occurred in the elderly population. Compared to the pre-PCV period (2000-2005), the odds ratio for non-PCV10 bacteraemia was 17.5 (CI 9.9-31.6; <i>P</i><0.001) in the late-PCV10 period, showing an overall increase in the proportion of bacteraemia cases being caused by non-vaccine serotype pneumococci (2016-2020). The increase in non-PCV10 serotypes is mainly driven by an expansion of lineage global pneumococcal sequencing cluster 3 (GPSC3) expressing serotype 8, alongside the emergence of serotype 12F that was mediated by multiple lineages (GPSC32/GPSC26/GPSC55). Both serotypes 8 and 12F were included in the latest PCV20 formulation that is licensed to be used in children and adults in Europe. Over 20 years, we observed a low prevalence of antimicrobial resistance (AMR) as predicted by genome data. There were no significant changes in AMR prevalence after vaccine introduction (<i>P</i>>0.05 for all comparisons). We saw a stably low prevalence of reduced penicillin susceptibility, which was observed in multiple pneumococcal lineages, with GPSC10 being the most common in the Gelderland collection, whilst GPSC1 and GPSC6 were common among the penicillin-resistant pneumococcal blood culture isolates provided by the Netherlands Reference Laboratory for Bacterial Meningitis. Comparison to global collections of GPSC10, GPSC1 and GPSC6 isolates favored the likelihood of separate introductions of penicillin-resistant isolates rather than cloncal expansion. Genomic surveillance of pneumococcal bacteraemia in this unbiased population sample in the Netherlands supports the use of higher valency PCVs, such as PCV20, especially in adults, to prevent future bacteraemia cases caused by <i>Streptococcus pneumoniae</i> in the Gelderland area, the Netherlands, while maintaining a low prevalence of AMR in the pneumococcal population.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657697","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":"Scalable genotyping of microbial colonies.","authors":"Arnold Chen, Nkazi Nchinda, Nate J Cira","doi":"10.1099/mgen.0.001378","DOIUrl":"10.1099/mgen.0.001378","url":null,"abstract":"<p><p>The sequence of the 16S region is taxonomically informative and widely used for genotyping microbes. While it is easy and inexpensive to genotype several isolates by Sanger sequencing the 16S region, this method becomes quite costly if scaled to many isolates. High-throughput sequencing provides one potential avenue for obtaining 16S sequences at scale but presents additional challenges. First, DNA purification workflows for high-throughput sample preparation are labour-intensive and expensive. Second, cost-effective multiplexing and library preparation schemes are difficult to implement for many libraries on a single sequencing run. Therefore, we implemented a scalable protocol for isolate genotyping involving colony polymerase chain reaction (PCR) with simple cell lysis as well as a four-barcode indexing scheme that enables scalable multiplexing and streamlined library preparation by amplifying with four primers simultaneously in a single reaction. We tested this protocol on 93 colonies cultured from environmental samples, and we were able to ascertain the identity of ~90% of microbial isolates.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664007","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 and phylogenetic analysis of hypervirulent <i>Klebsiella pneumoniae</i> ST23 in Ireland.","authors":"Mark Maguire, Niall DeLappe, Christina Clarke, Alma Touhy, Ulrike Carlino-MacDonald, Alan Hutson, Martin Cormican, Wendy Brennan, Genevieve Devane, Dearbháile Morris, Simone C Coughlan, Georgios Miliotis, Thomas A Russo, Liam P Burke","doi":"10.1099/mgen.0.001373","DOIUrl":"https://doi.org/10.1099/mgen.0.001373","url":null,"abstract":"<p><p>Hypervirulent <i>Klebsiella pneumoniae</i> (hv<i>Kp</i>) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hv<i>Kp</i> sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 <i>K. pneumoniae</i> ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (<i>n</i>=59), invasive infections (<i>n</i>=18), non-invasive sites (<i>n</i>=12) and the hospital environment (<i>n</i>=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The <i>in vivo</i> virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (<i>bla</i> _OXA-48/<i>bla</i> _OXA-181/<i>bla</i> _NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar <i>in vivo</i> virulence. An established clone of hv<i>Kp</i> ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hv<i>Kp</i> makes its detection and control in the healthcare setting challenging.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664003","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":"Plasmid conjugation drives within-patient plasmid diversity.","authors":"Fan Grayson, Leo Loman, Toby Nonnenmacher, Diane Pople, Jack Pollard, Bharat Patel, David Williams, Luke Hounsome, Katie L Hopkins, Julie V Robotham, Alice Ledda","doi":"10.1099/mgen.0.001361","DOIUrl":"10.1099/mgen.0.001361","url":null,"abstract":"<p><p>Plasmids are well-known vehicles of antimicrobial resistance (AMR) gene dissemination. Through conjugation, plasmid-encoded AMR genes are spread among neighbouring bacteria, irrespective of their strain or even their species. This process is very concerning from a public health perspective, as plasmid-borne AMR gene outbreaks are often not confined to single species or strains and are therefore more difficult to fully uncover. At the moment, the impact of plasmid conjugation on within-patient plasmid diversity is not well understood. In this work, we will tackle the role of conjugation on within-patient plasmid diversity using a dataset of carbapenemase-producing <i>Enterobacterales</i>. The dataset of 256 sequences originates from bacterial isolates cultured from 115 English patients over 30 months. Each patient has more than one sequence, with at least one sequence carrying an OXA-48 gene, a well-known plasmid-borne carbapenemase-encoding gene. If more than one sequence carries the OXA-48 gene, they are carried in different bacterial hosts. Using a hybrid <i>de novo</i>-on-reference assembly pipeline, we were able to reconstruct the full OXA-48 plasmid from short read sequencing data for 232 of the 256 sequences. Of the 115 patients, 83 (72%) patients had an identical OXA-48 plasmid in two or more sequences. Only two patients carried very different (<i>></i>200 SNPs) alleles of the OXA-48 plasmid, probably from separate acquisitions. Our study shows that when more than one bacterial host carrying an OXA-48 plasmid is found in a patient, it is most likely that the same plasmid has been shared via conjugation. The event of separate acquisition of different plasmids in different bacterial hosts is highly unlikely in our dataset.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664005","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}