Microbial Genomics最新文献

{"title":"'Vivaldi': an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2.","authors":"C Patrick McClure, Theocharis Tsoleridis, Jack D Hill, Nadine Holmes, Joseph G Chappell, Timothy Byaruhanga, Joshua Duncan, Miruna Tofan, Louise Berry, Gemma Clark, William L Irving, Alexander W Tarr, Jonathan K Ball, Stuart Astbury, Matt Loose","doi":"10.1099/mgen.0.001451","DOIUrl":"10.1099/mgen.0.001451","url":null,"abstract":"<p><p>Prior to the emergence of SARS-CoV-2 in 2019, alphacoronaviruses 229E and NL63 and betacoronaviruses OC43 and HKU1 were already established endemic 'common cold' viral infections. Despite their collective contribution towards global respiratory morbidity and mortality and potential to inform the future trajectory of SARS-CoV-2 endemicity, they are infrequently sequenced. We therefore developed a 1,200 bp amplicon whole-genome sequencing scheme targeting all four seasonal coronaviruses and SARS-CoV-2. The 'Vivaldi' method was applied retrospectively and prospectively using Oxford Nanopore Technology to ~400 seasonal coronavirus infections diagnosed in Nottingham, UK, from February 2016 to July 2023. We demonstrate that the amplicon multiplex strategy can be applied agnostically to determine the complete genomes of five different species from two coronaviral genera. Three hundred and four unique seasonal coronavirus genomes of greater than 95% coverage were achieved: 64 for 229E, 85 for NL63, 128 for OC43 and 27 for HKU1. They collectively indicated a dynamic seasonal coronavirus genomic landscape, with co-circulation of multiple variants emerging and declining over the UK winter respiratory infection season, with further geographical distinction when compared to a global dataset. Prolonged infection with concomitant intra-host evolution was also observed for both alpha- (NL63) and betacoronaviruses (OC43). This data represents the largest single cohort of seasonal coronavirus genomes to date and also a novel amplicon scheme for their future global surveillance suitable for widespread and easy adoption in the post-SARS-CoV-2 era of viral genomics.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642930","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":"Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.","authors":"Yasemin Coşgun, Süleyman Yalçın, Ege Dedeoğlu, Gültekin Ünal, Katharina Kopp, Biran Musul, Ekrem Sağtaş, Philomena Raftery, Gülay Korukluoğlu, Sedat Kaygusuz","doi":"10.1099/mgen.0.001357","DOIUrl":"10.1099/mgen.0.001357","url":null,"abstract":"<p><p>During the COVID-19 pandemic, next-generation sequencing (NGS) has been instrumental for public health laboratories in tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations and informing responses. Illumina systems and Oxford Nanopore Technologies (ONT) have been primary tools for NGS, each presenting unique advantages. The hybrid assembly (HA) approach, integrating short- and long-read sequencing methods, has been developed to improve genome accuracy by utilizing the combined advantages of both techniques. While HA has been used to enhance SARS-CoV-2 genome quality, its optimal applications for SARS-CoV-2 sequencing and surveillance have not been systematically studied. This study seeks to address this gap by evaluating the conditions under which HA improves SARS-CoV-2 genomic surveillance, analysing 192 samples using eight bioinformatics methods across both platforms. HA was evaluated against single-technology approaches for its genome assembly and mutation detection performance. While HA did not outperform single-technology methods in detecting unique mutations, it produced marginally more complete genomes than Illumina-based methods. Importantly, mutations identified by HA were consistently detected across all eight methodologies, demonstrating its reliability in mutation detection. Moreover, our research underlines the critical need for in-house validation of methods and exposes the limitations inherent in proprietary pipelines. Our findings suggest that an HA approach could be used as a quality control tool in genomic surveillance, particularly for improving low-quality ONT sequencing data by integrating high-quality Illumina sequencing data. However, implementing HA demands the presence of both sequencing platforms and additional resources, such as hands-on time, expensive sequencing reagents and bioinformatics know-how. A decision-tree analysis identified the percentage of trimmed ONT reads relative to total reads as crucial for HA success, emphasizing the significance of high-quality ONT reads. This comprehensive approach provides public health laboratories insights to refine genomic surveillance strategies for SARS-CoV-2, potentially influencing future research and response efforts.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12244368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144600864","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 analysis and pneumococcal population dynamics across PCV implementation in South Korea, 1997-2023.","authors":"Jeong-Ih Shin, Sung-Yeon Cho, Jiyon Chu, Chulmin Park, Minho Lee, Joon Young Song, Seung-Hyun Jung, Dong-Gun Lee","doi":"10.1099/mgen.0.001433","DOIUrl":"10.1099/mgen.0.001433","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i>, a clinically significant pathogen, causes invasive diseases in children and older adults. Pneumococcal conjugate vaccines (PCVs) have substantially reduced the incidence of vaccine serotype (VT) pneumococcal diseases. However, serotype replacement, characterized by the emergence of non-vaccine serotypes (NVTs), presents a persistent challenge to disease prevention. To address this, we analysed 236 pneumococcal isolates collected in South Korea between 1997 and 2023, spanning both pre- and post-PCV13 periods. Whole-genome sequencing was performed to assess serotypes, antimicrobial resistance, virulence factors and global pneumococcal sequence clusters (GPSCs). Capsular switching events and the relationships among pneumococcal lineages, serotypes and disease invasiveness were also evaluated. Among the 37 identified serotypes, NVTs such as 23A, 15B/15C and 10A were dominant post-PCV13. Serotype 10A, associated with invasive pneumococcal diseases (IPDs), belonged to GPSC634-ST11189 and showed elevated minimum inhibitory concentrations for <i>β</i>-lactams. Capsular switching events were observed between VTs and NVTs, highlighting the adaptability of pneumococcal populations. Antimicrobial non-susceptibility was highest for azithromycin (82.7%), followed by tetracycline (76.5%) and co-trimoxazole (70.4%), with higher rates observed in the post-PCV13 period. Notably, amoxicillin (<i>P</i>=0.049) and meropenem (<i>P</i>=0.002) showed significant non-susceptibility in the post-PCV13 period. Virulence factors <i>pspA</i> and <i>pfbA</i> were associated with IPDs, while pilus islet PI-1-related genes were more frequent in non-invasive cases. These findings underscore the importance of genomic surveillance to monitor pneumococcal population dynamics and inform public health strategies. The inclusion of serotype 10A in the recently approved PCV20 offers promise for further reducing the global burden of IPDs, including in South Korea.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649884","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":"Large-scale global molecular epidemiology of antibiotic resistance determinants in <i>Streptococcus pneumoniae</i>.","authors":"Kazi Shefaul Mulk Shawrob, Achal Dhariwal, Gabriela Salvadori, Rebecca A Gladstone, Roger Junges","doi":"10.1099/mgen.0.001444","DOIUrl":"10.1099/mgen.0.001444","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i> is a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts for this microbe. Leveraging publicly available whole-genome sequencing (WGS) data, we aimed to investigate the presence and distribution patterns of antibiotic resistance determinants in <i>S. pneumoniae</i> with a focus on multidrug resistance (MDR) and serotype distribution. Metadata and genomes were obtained from the National Center for Biotechnology Information Pathogen Detection database. Curation and harmonization were performed in R and SPSS. Data on resistance patterns were defined according to AMRFinderPlus, and a combination of prediction tools was employed for <i>in silico</i> serotyping. Analyses involved 75,161 genomes totalling 122,673 gene/allele counts from 14 antibiotic classes. MDR was observed in 16.7% of isolates, with the highest increasing rates in Asia and South America. Within antibiotic classes, an increase in macrolide resistance genes was highlighted, particularly in the proportion of genomes presenting <i>mef(A</i>)/<i>msr(D</i>). Over a third of isolates with serotypes 19F, 23F, 15A, 6B and 19A showed MDR. We further observed the highest significant increases in the presence of resistance in 33F, 22F, 10A and 23A. Serotype 13, not included in any vaccine formulation, presented high MDR rates with a strong increasing trend. The findings of this study highlight variations in resistance determinants globally and across serotypes over time. Collectively, these data underscore the added value of utilizing public WGS data to investigate the effectiveness and repercussions of treatment and vaccination strategies on managing antibiotic resistance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553965","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 epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020-December 2022.","authors":"Eleanor H Hayles, Andrew J Page, Robert A Kingsley, Javier Guitian, The Covid-Genomics Uk Consortium, Gemma C Langridge","doi":"10.1099/mgen.0.001435","DOIUrl":"10.1099/mgen.0.001435","url":null,"abstract":"<p><p>In the UK, the COVID-19 Genomics UK Consortium (COG-UK) established a real-time national genomic surveillance system during the COVID-19 pandemic, producing centralized data for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a COG-UK partner, Quadram Institute Bioscience in Norfolk sequenced over 87,000 SARS-CoV-2 genomes as part of the national effort, contributing to the region becoming densely sequenced. Retrospective analysis of SARS-CoV-2 lineage dynamics in this region may contribute to preparedness for future pandemics. In total, 29,406 SARS-CoV-2 whole genome sequences and corresponding metadata from Norfolk were extracted from the COG-UK dataset, sampled between March 2020 and December 2022, representing 9.9% of regional COVID-19 cases. Sequences were lineage typed using Pangolin, with subsequent lineage analysis carried out in R using RStudio and related packages, including graphical analysis using ggplot2. In total, 401 global lineages were identified, with 69.8% appearing more than once and 31.2% over ten times. Temporal clustering identified six lineage communities based on first lineage emergence. Alpha, Delta and Omicron variants of concern (VOCs) accounted for 8.6, 34.9 and 48.5% of sequences, respectively. These formed four regional epidemic waves alongside the remaining lineages which were observed in the early pandemic prior to VOC designation and were termed 'pre-VOC' lineages. Regional comparison highlighted variability in VOC epidemic wave dates dependent on location. This study is the first to assess SARS-CoV-2 diversity in Norfolk across a large timescale within the COVID-19 pandemic. SARS-CoV-2 was both highly diverse and dynamic throughout the Norfolk region between March 2020 and December 2022, with a strong VOC presence within the latter two-thirds of the study period. The study also displays the utility of incorporating genomic epidemiological methods into pandemic response.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642928","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 surveillance of invasive <i>Streptococcus pneumoniae</i> strains in south Tunisia during 2012-2022.","authors":"Fahmi Smaoui, Boutheina Ksibi, NourElhouda Ben Ayed, Sonia Ktari, Omar Gargouri, Senda Mezghani, Basma Mnif, Faouzia Mahjoubi, Héla Karray, Adnene Hammami","doi":"10.1099/mgen.0.001448","DOIUrl":"https://doi.org/10.1099/mgen.0.001448","url":null,"abstract":"<p><p><b>Purpose.</b> Invasive pneumococcal disease (IPD) remains a major global public health concern due to its high morbidity and mortality rates, particularly among children and the elderly. This study aimed to apply whole-genome sequencing (WGS) to characterize <i>Streptococcus pneumoniae</i> strains responsible for IPD in south Tunisia, including serotype distribution, clonal relationship and antimicrobial resistance (AMR) profiles.<b>Methods.</b> A total of 148 IPD <i>S. pneumoniae</i> isolates were collected from the microbiology laboratory at Habib Bourguiba University Hospital in Sfax, Tunisia, between 2012 and 2022. These isolates underwent WGS using Illumina technology. Bioinformatic analyses were performed to determine serotype distribution, sequence types (STs), Global Pneumococcal Sequence Clusters (GPSCs), phylogenetic relationships and AMR determinants.<b>Results.</b> Twenty-six different serotypes were identified, with the most prevalent being 14 (18%), 3 (13%), 19A (12%) and 19F (11%). The isolates showed high genomic diversity, as they belonged to 32 GPSCs and 59 STs. The most common GPSCs were GPSC-6, GPSC-10 and GPSC-44, associated with serotypes 14, 19A and 19F, respectively. The most frequent STs were ST2918, ST179 and ST3772. The most common resistance genes were <i>erm</i>B (53%) and <i>tet</i>M (55%), which were linked to resistance against erythromycin and tetracycline, respectively. There was a considerable concordance between WGS-based and phenotypic resistance profiles for most tested antibiotics, with few major and very major errors for most antibiotics. Temporal analysis showed a decline in serotypes 19F and 9V throughout the study period, which was associated with slight decreases in GPSC-6 and GPSC-44, while serotype 19A and GPSC-10 sharply increased.<b>Conclusion.</b> This study highlights the substantial genomic diversity, serotype distribution and high prevalence of AMR among IPD <i>S. pneumoniae</i> isolates in south Tunisia, underscoring the need for continued surveillance and effective vaccination strategies to combat this persistent public health threat.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649885","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":"Reconstructing NOD-like receptor alleles with high internal conservation in <i>Podospora anserina</i> using long-read sequencing.","authors":"S Lorena Ament-Velásquez, Brendan Furneaux, Sonia Dheur, Alexandra Granger-Farbos, Rike Stelkens, Hanna Johannesson, Sven J Saupe","doi":"10.1099/mgen.0.001442","DOIUrl":"10.1099/mgen.0.001442","url":null,"abstract":"<p><p>NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defence mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self-/non-self-recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The <i>het-d</i> and <i>het-e</i> NLRs in <i>Podospora anserina</i> are highly polymorphic incompatibility genes (<i>het</i> genes) whose products recognize different allelic variants of the HET-C protein via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here, we confirm that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic <i>het-d</i> and <i>het-e</i> incompatibility reactions. AlphaFold 3 structure models suggest that their WD40 domain folds into two 7-blade <i>β</i>-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular <i>het-e</i> allele does not have an incompatibility reaction with common <i>het-c</i> alleles, despite being 11-repeats long. Finally, we present evidence that the recognition phenotypes of <i>het-e</i> and <i>het-d</i> arose through convergent evolution. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of <i>het</i> NLRs, while also highlighting both the fragility and the flexibility of <i>β</i>-propellers as immune sensor domains.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12222747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553966","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":"Insights into microbial dysbiosis and <i>Cutibacterium acnes</i> CAMP factor interactions in acne vulgaris.","authors":"Qi Chen, Congyu Liu, Juan Tao, Weihong Zeng, Zhongliang Zhu, Chengbing Yao, Yuhua Shang, Jun Tang, Tengchuan Jin","doi":"10.1099/mgen.0.001449","DOIUrl":"10.1099/mgen.0.001449","url":null,"abstract":"<p><p>Acne vulgaris is a common skin condition marked by the formation of comedones, papules, pustules and nodules, with its underlying causes still not fully understood. This study explores the impact of microbial dysbiosis and virulence factors on acne development. Through high-throughput 16S rRNA sequencing, we identified significant disruptions in the skin microbiome, particularly in comedones. Key virulence factors of <i>Cutibacterium acnes</i>, known as Christie-Atkins-Munch-Peterson (CAMP) factors, were assessed using both <i>in vitro</i> and <i>in vivo</i> models. Among these, CAMP2 and CAMP5 demonstrated the highest inflammatory and haemolytic activities in keratinocytes. Topical anti-IL-8 treatment in a murine model effectively reduced inflammation and suppressed CAMP expression. Structural analysis of CAMP3 uncovered distinct pathogenic features that, alongside CAMP5, were found to aggravate acne-like inflammation and sebaceous gland atrophy. These findings advance our understanding of the interplay between microbial dysbiosis and CAMP factors in acne pathogenesis, offering potential avenues for therapeutic intervention.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642929","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":"Phylogenomics, evolution and origin of multidrug-resistant <i>Acinetobacter baumannii</i> ST15.","authors":"Eradah Abu Sabah, Liam A Tobin, Francois Lebreton, Patrick T McGann, Mehrad Hamidian","doi":"10.1099/mgen.0.001450","DOIUrl":"10.1099/mgen.0.001450","url":null,"abstract":"<p><p>We studied the genomic evolution and transmission dynamics of multidrug-resistant ST15 (Institut Pasteur scheme) <i>Acinetobacter baumannii</i>, examining resistance gene acquisition, clonal diversification, geographic distribution and origin of this high-risk clone. One hundred and fifty-two (<i>n</i>=152) ST15 genomes from 18 countries (1997-2024), including 42 isolates from U.S. Military Treatment Facilities and 110 publicly available genomes in GenBank, were analysed. Whole-genome sequencing, assembly and annotation were performed using established bioinformatics pipelines. Phylogenetic analysis based on core-genome SNPs - filtered for recombination with <i>Gubbins</i> - was combined with mobile element and resistance gene identification. ST15 isolates separated into two main clades with distinct subclades and variable resistance profiles. Homologous recombination drove the diversification of resistance determinants, including multiple <i>ampC</i> alleles. Key resistance genes, such as <i>bla</i> _OXA-23, were disseminated via known transposons (Tn<i>2006</i> or Tn<i>2008</i>), while plasmid exchange, including <i>dif</i> module acquisitions, also played a role in the spread of <i>bla</i> _CARB. Patristic analysis identified Argentina as the likely origin for the emergence of ST15, aligning with early 1997 isolates. Recombination, transposon-mediated gene transfer and plasmid exchange have been central in driving the evolution and global dissemination of ST15.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649887","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":"Molecular characterization and prevalence of plasmids co-harbouring <i>mcr</i> and ESBL genes.","authors":"K M G Houkes, V Weterings, J J Verweij, J L Murk, W van den Bijllaardt, J J J M Stohr","doi":"10.1099/mgen.0.001458","DOIUrl":"https://doi.org/10.1099/mgen.0.001458","url":null,"abstract":"<p><p>Multidrug-resistant Enterobacterales isolates carrying extended-spectrum beta-lactamases (ESBLs) and mobile colistin resistance (<i>mcr</i>) genes pose a significant healthcare threat as they can lead to difficult-to-treat infections. This study investigates the prevalence of isolates co-harbouring ESBL and <i>mcr</i> genes and characterizes the plasmids co-harbouring those genes. ESBL-producing Enterobacterales (ESBL-E) isolates identified during point prevalence surveys (PPS) in a Dutch hospital were screened for <i>mcr</i> genes. Plasmids co-harbouring <i>mcr</i> and ESBL genes were identified using long- and short-read sequencing data, while detecting resistance and replicon genes using AMRFinderPlus and PlasmidFinder. The plasmid database PLSDB was searched for plasmids containing the same <i>mcr</i> and ESBL gene(s), and SNP and DCJ-Indel distance analyses were conducted to examine plasmid diversity. The most recent common ancestor (MRCA) was inferred through timed phylogeny analyses in BEAST, and putative composite transposons containing the <i>mcr</i> or ESBL genes were identified. Among 188 screened ESBL-E, 11 harboured <i>mcr</i> genes: 9 with <i>mcr-9</i> and 2 with <i>mcr-9</i> and <i>mcr-4.3</i>. All plasmids containing <i>mcr</i> and ESBL genes were IncHI plasmids harbouring <i>mcr-9</i>, <i>bla</i> _CTX-M-9 and/or <i>bla</i> _SHV-12. The plasmid database search resulted in 128 similar plasmids. SNP analysis showed ≤10 SNPs among the PPS study plasmids and up to 924 SNPs among all plasmids. Structural relatedness and phylogenetic analyses revealed clustering of the PPS study plasmids but no additional taxonomical or geographical clustering. The MRCA of the PPS study plasmids likely emerged between 1986 and 2008. Finally, composite transposon analysis indicated that matching complete insertion sequences rarely flanked <i>mcr-9</i> genes, whereas <i>bla</i> _CTX-M-9 and <i>bla</i> _SHV-12 frequently were. The prevalence of <i>mcr</i> genes among ESBL-E in this study is 5.9%, with <i>mcr-9</i> being the most prevalent. Limited plasmid diversity suggests a single introduction event followed by regional and global dissemination across related bacterial species. Persistent ESBL gene mobility suggests a more recent introduction of these genes compared to the <i>mcr-9</i> genes.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732108","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}