Microbial Genomics最新文献

{"title":"Genomic surveillance reveals long-term endemicity and outbreak potential of <i>Klebsiella pneumoniae</i> sequence type 48 in a German hospital and its global context.","authors":"Ngoc Minh Nguyen, Anna Weber, Basil Britto Xavier, Juan Pablo Rodríguez-Ruiz, Axel Kola, Michael Behnke, Christine Geffers, Herman Goossens, Stephan Harbarth, Marc Bonten, Rafael Canton, Petra Gastmeier, Youri Glupczynski, Friederike Maechler, Surbhi Malhotra-Kumar, On Behalf Of The R-Gnosis Wp Starcs Wp And Mistar Wp Study Groups","doi":"10.1099/mgen.0.001707","DOIUrl":"10.1099/mgen.0.001707","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> sequence type 48 (Kp-ST48) is a globally distributed clone linked to antimicrobial resistance (AMR) yet lacks a comprehensive genomic analysis. Here, we investigated the persistence, transmission dynamics and global context of ST48 in a large tertiary hospital in Berlin, Germany. Between 2014 and 2022, 48 surveillance and 15 putative outbreak Kp-ST48 isolates were isolated in a tertiary care, multi-site hospital in Berlin, Germany. Genomic diversity was analysed by short- and long-read sequencing. Additionally, we included 223 publicly available Kp-ST48 genomes from five continents over 40 years (1982-2022) in the phylodynamic analysis. We identified two genetically distinct clades (A and B) within the global Kp-ST48 population. The global spread of Kp-ST48 was driven by clade B, which included all the genomes from the Berlin hospital. Two hospital-specific lineages (1 and 2) were identified with distinct population dynamics. Lineage 2 was transient and linked to a putative outbreak in 2019. Meanwhile, lineage 1 was first detected in 2014 and persisted for over 8 years until 2022, with multiple putative patient-to-patient and indirect transmission events identified. Carbapenem resistance determinants (<i>ompK35/36</i> mutations, <i>bla</i> _KPC, <i>bla</i> _NDM, <i>bla</i> _OXA-48, <i>bla</i> _VIM) were present in 57% (<i>n</i>=163/286) of genomes, and up to three <i>bla</i> _CTX-M-15 copies were found integrated into chromosomes. Although Kp-ST48 generally did not contain a high number of virulence genes, 19 genomes showed potential for AMR-hypervirulence convergence. This study reveals the endemic persistence with outbreak potentials of Kp-ST48 in a hospital over 8 years, characterized by high genome plasticity. Our results highlight the global distribution of this clone, which warrants continuous surveillance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13384113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148520668","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":"Stabilizing features of cefotaximase harbouring plasmids enable persistence in UK livestock.","authors":"Nicholas Duggett, Daisy E Gates, Manal AbuOun, Jeremy Chanter, Chris Teale, Javier Nunez-Garcia, Muna F Anjum","doi":"10.1099/mgen.0.001775","DOIUrl":"10.1099/mgen.0.001775","url":null,"abstract":"<p><p>Extended-spectrum cephalosporinases (ESCs) confer resistance to a range of beta-lactam compounds, including many cephalosporins and have grown in prevalence since the early 2000s. ESCs are often disseminated via plasmids, which can also encode other genes that confer bacterial fitness. Until recently, detailed characterization of plasmids encoding antimicrobial resistance genes was limited by the technical ability to close plasmid genomes. Recent advances in long-read technology have simplified this problem, facilitating the characterization of the genetic structure of plasmids and their component genes. This study examined the genetic mechanisms that underpin the stability of the most common cefotaximase-encoding plasmids in <i>Escherichia coli</i> recovered from UK livestock between 2013 and 2020. The most common plasmid replicon types were IncF, IncI1 and IncX, and the predominant cefotaximases were <i>bla</i> _CTX-M-1, <i>blaCTX-M-14</i>, <i>bla</i> _CTX-M-15 and <i>bla</i> _CTX-M-55; in this study, we focused on IncI1 plasmids only which were most commonly associated with the cefotaximases in our dataset. Comparison of circularized plasmid genomes revealed that IncI1/<i>bla</i> _CTX-M-1 plasmids showed a high degree of genetic similarity to one another in the time period examined, as did IncI1/<i>bla</i> _CTX-M-14 plasmids, indicating stability of these plasmid genomes. Overall, our results indicate that IncI1/<i>bla</i> _CTX-M-1 plasmids carry genes promoting their maintenance in host <i>E. coli</i> and encode several genes that may enhance their fitness. Therefore, these plasmids may play an important role in the persistence of ESC resistance in <i>E. coli</i> isolated from One-Health compartments, despite nationwide reductions in cephalosporin usage in both humans and livestock.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13341076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148396831","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 epidemiology reveals distinct lineages and genomic profiles of avian pathogenic and commensal <i>Escherichia coli</i> in broiler flocks.","authors":"Homayoon Davam, Désirée S Jansson, Emma Nord, Peter Halvarsson, Robert Söderlund, Jesper Rydén, Ingrid Hansson","doi":"10.1099/mgen.0.001797","DOIUrl":"10.1099/mgen.0.001797","url":null,"abstract":"<p><p><i>Escherichia coli</i> is predominantly an intestinal commensal; however, avian pathogenic <i>E. coli</i> (APEC) causes colibacillosis in poultry. The APEC pathotype lacks a clear genetic definition, further complicated by its opportunistic nature. To compare the genomic characteristics of avian pathogenic and commensal <i>E. coli</i>, isolates from diseased and healthy broiler flocks in Sweden were analysed, collected between 2022 and 2024. Clinical isolates (<i>n</i>=202) were collected at necropsy from 40 flocks during colibacillosis outbreaks, and non-clinical isolates (<i>n</i>=109) were obtained from litter using sock sampling in 60 unaffected flocks. Whole-genome sequencing was performed to determine sequence types (STs), serotypes, phylogroups, virulence-associated genes (VAGs) and to identify ColV plasmids. A five-gene APEC marker panel targeting plasmid-associated virulence genes (<i>iutA, hlyF, iss, iroN</i> and <i>ompT</i>) was used to classify isolates as APEC or non-APEC, and high-risk clones were identified according to the APECtyper scheme. Clinical isolates comprised 22 STs and 25 serotypes and were dominated (59%) by the ST23 O78:H4 clone within phylogroup C. Non-clinical isolates were more diverse (44 STs, 67 serotypes), primarily within phylogroups A (48%) and B1 (33%), with no clone predominating. Clinical isolates carried significantly more VAGs (<i>P</i><0.001). Overall, 97% of clinical isolates were identified as APEC, all of which carried a ColV plasmid. Among non-clinical isolates, 28% were APEC, of which 80% were ColV-positive. However, clinical APEC isolates carried significantly more ColV-associated virulence gene clusters than non-clinical APEC isolates (<i>P</i><0.001). Only 5% of non-APEC isolates were ColV-positive. High-risk clones were restricted to clinical APEC isolates (63%). These findings indicate that colibacillosis in Swedish broilers was largely driven by a dominant APEC clone during the study period, highlighting the need for coordinated surveillance and targeted control of high-risk clones. The presence of VAG reservoirs among isolates from unaffected flocks, together with the limitations of marker-based APEC typing, supports integrated frameworks combining lineage, VAG profiles and plasmid content for more reliable APEC identification and pathogenicity assessment.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13401734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562491","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":"High-precision binary trait association on phylogenetic trees.","authors":"Ishaq O Balogun, Christopher P Mancuso, Tami D Lieberman","doi":"10.1099/mgen.0.001791","DOIUrl":"10.1099/mgen.0.001791","url":null,"abstract":"<p><p>Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wide association study (mGWAS) methods have been developed to account for the fact that genome-wide linkage in bacteria creates strong evolutionary-induced associations, these methods have high false discovery rates or lack statistical power, have poor performance on negative interactions and face computational limits at the scale required for pangenome-wide study of gene-gene interactions. Here, we present Simulation-based Phylogenetic iNteraction Inference (SimPhyNI), a computationally optimized framework for efficient and rigorous mGWAS studies. SimPhyNI builds null co-occurrence distributions by independently simulating traits using phylogenetically informed parameters, novelly including time to first event. The constrained variation in these simulations, combined with log odds ratio scoring for comparing across traits, robustly identifies both positive and negative associations. Using synthetic datasets mimicking both gene-gene and gene-trait associations, we demonstrate that SimPhyNI achieves high precision and recall for both positive and negative interactions. We demonstrate SimPhyNI's utility by detecting interactions between phage defence systems in <i>Escherichia coli</i> and gene-gene interactions across the entire <i>E. coli</i> pangenome (>9 million tests). Though developed here for binary traits, SimPhyNI's design supports extension to multi-state and continuous traits using generalized models of stochastic simulation. SimPhyNI's performance and scalability enable genome-wide discovery of genetic interactions that drive microbial function, ecology and disease.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148631029","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":"Mobile genetic element diversity across Shiga toxin-producing <i>Escherichia coli</i> lineages in French cattle.","authors":"Fabien Vorimore, Mai-Lan Tran, Sandra Jaudou, Patrick Fach, Sabine Delannoy","doi":"10.1099/mgen.0.001794","DOIUrl":"10.1099/mgen.0.001794","url":null,"abstract":"<p><p>Shiga toxin-producing <i>Escherichia coli</i> (STEC) represent a genetically diverse group of pathogens whose virulence is largely driven by mobile genetic elements (MGEs), including plasmids and bacteriophages. While horizontal gene transfer is central to STEC evolution, the extent to which virulence-associated MGEs circulate within natural reservoirs remains poorly understood. In this study, we investigated the diversity, distribution and lineage associations of MGEs in a collection of 73 <i>E. coli</i> strains isolated from cattle in France, a major reservoir for pathogenic STEC. Using both short-read and long-read whole-genome sequencing, we characterized plasmid content, prophage repertoires and <i>stx</i>-encoding phages and examined their relationships with strain phylogeny. We observed a high diversity of plasmids, with individual strains carrying up to four large plasmids, alongside an even greater diversity of prophages. Despite this diversity, some associations were identified between specific virulence plasmid groups, Stx phage types and defined pathogroups or lineages. These patterns were supported by the congruence between core-genome and accessory-genome phylogenies, suggesting long-term evolutionary coupling rather than frequent exchange of entire MGEs. In contrast, some non-virulence plasmids were broadly distributed, consistent with more general selective advantages. Notably, we identified enterohaemorrhagic <i>E. coli</i> strains (<i>stx</i>- and <i>eae</i>-positive strains) in atypical phylogenetic backgrounds, highlighting the capacity for virulence determinants to emerge in diverse lineages, while underscoring the constraints that limit their stable establishment, as their long-term persistence appears limited to specific genetic backgrounds. Together, our findings indicate that the circulation of virulence-associated MGEs in the bovine reservoir is constrained by ecological and evolutionary factors.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549448","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":"Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant <i>Enterococcus faecium</i>.","authors":"Emma G Mills, Kirsten M Evans, Ava J Dorazio, Kevin M Squires, Alexander J Sundermann, Madison E Stellfox, Matthew J Culyba, Ryan K Shields, Daria Van Tyne","doi":"10.1099/mgen.0.001778","DOIUrl":"10.1099/mgen.0.001778","url":null,"abstract":"<p><p>Colonization of the gastrointestinal (GI) tract by vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity and can miss transmission involving low-abundance and co-colonizing strains. Here, we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures obtained between 2020 and 2025 at a single hospital. GI tract populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters including 6 clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13331451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148376336","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":"Tn<i>3</i>-derived inverted-repeat miniature elements that mobilize antibiotic resistance genes.","authors":"Ryota Gomi, Hirokazu Yano","doi":"10.1099/mgen.0.001790","DOIUrl":"10.1099/mgen.0.001790","url":null,"abstract":"<p><p>Miniature inverted-repeat transposable elements (MITEs) are non-autonomous mobile genetic elements (MGEs) that can be mobilized by transposases provided by the relevant autonomous MGEs. MITEs originating from Tn<i>3</i>-family transposons were previously termed Tn<i>3</i>-derived inverted-repeat miniature elements (TIMEs). Composite transposon-like structures bounded by two copies of TIME, called TIME-COMPs, were shown to mobilize the intervening sequences. However, their association with antibiotic resistance genes (ARGs) has not yet been systematically studied. This study thus aimed to identify new TIME-COMP-like structures containing ARGs in the genomic sequences of the clinically important bacterial family <i>Enterobacteriaceae</i> in public databases. TIME-COMP-like structures were first searched for in the plasmid database PLSDB, focusing on small plasmids, using a self-against-self blastn approach to identify repeated elements. Then, newly and previously identified MITEs (including TIMEs) were searched for in the NCBI core nucleotide database to identify TIME-COMP-like structures located on other replicons. Bioinformatic analysis identified multiple previously unreported TIME-COMPs containing ARGs, which are bounded by directly or inversely oriented TIMEs, namely IS<i>101</i>, MITESen1 and a novel 244 bp TIME termed TIME244. TIME244 contains a putative resolution site related to that of Tn<i>21</i>. These TIMEs were predominantly detected in plasmids and very rarely in chromosomes. The ARGs embedded in newly identified TIME-COMPs were <i>bla</i> _KPC-2, <i>floR</i>, <i>qnrS1</i> and <i>tet</i>(A). Notably, the <i>bla</i> _KPC-2 carbapenemase gene was found in TIME-COMPs bounded by TIME244 and a TIME-COMP bounded by IS<i>101</i>. These findings highlight a potential role for TIMEs in the spread of diverse ARGs.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13367494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437530","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":"Phylogenomic analysis of a methicillin-resistant <i>Staphylococcus aureus</i> ST764 isolate from Thailand in global context reveals limited cross-border transmission.","authors":"Thidarat Netikul, Bharkbhoom Jaemsai, Wuthiwat Ruangchai, Thanakron Noppanamas, Sumalee Kondo, Lalita Narachasima, Prasit Palittapongarnpim","doi":"10.1099/mgen.0.001774","DOIUrl":"10.1099/mgen.0.001774","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) ST764, a variant of ST5, has emerged and spread in Japan and China. We investigated the genome of a Thai isolate (SATU136) and the global phylogeny of ST764 to understand its global transmission history. The complete genome of SATU136 consists of a 2.89 Mb chromosome with a type II SCC<i>mec</i> element and a <i>qacB</i>-carrying plasmid but lacks the arginine catabolic mobile element (ACME). Based on the currently available global dataset, phylogenetic and phylodynamic analyses suggest that ST764 emerged in Japan in the early 1980s and was subsequently inferred to have disseminated to China and Thailand during the 1990s and early 2000s, coinciding with a peak in its overall effective population size. After this period, transmission was inferred to have become more geographically structured, with distinct clades forming in each country. Although cross-country transmission was inferred to be limited overall, onward dissemination to non-Asian countries was also detected within the Thailand-associated lineage. In contrast, the ACME element remained confined to a single Japanese subclade, with currently no evidence of spread beyond Japan. The relatively structured geographic distribution of ST764 offers a window for early detection upon introduction to new countries, which may facilitate control of its spread.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471358","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 pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements.","authors":"Victoria T Orr, Ellie Harrison, Damian W Rivett, Rosanna C T Wright, James P J Hall","doi":"10.1099/mgen.0.001789","DOIUrl":"10.1099/mgen.0.001789","url":null,"abstract":"<p><p>Plasmids are extrachromosomal mobile genetic elements that can facilitate rapid bacterial adaptation by transferring genes between individuals. Whilst plasmids are known to exist in diverse habitats and encode a range of traits, most of our knowledge about plasmids comes from clinically associated antimicrobial resistance (AMR) plasmids that have already been recruited as vectors of drug resistance and have likely been shaped by strong selection for plasmid-encoded antibiotic resistance. Here, we investigated 26 plasmids from the pQBR collection - a set of large, co-existing mercury resistance environmental plasmids isolated in <i>Pseudomonas</i> spp. from a field in Oxfordshire in the 1990s - and explored the ability of pQBR plasmids to transfer novel chromosomally encoded traits. New whole-genome sequences for 25 plasmids confirmed that these soil-isolated plasmids are generally very large (140-588 kb), constitute at least six distinct genetic groups and have relatives in various other <i>Pseudomonas</i> species and habitats. Despite significant nucleotide-level divergence, Groups I (pQBR103-like, ~406 kb) and IV (pQBR57-like, ~328 kb) showed remarkable ancient similarities in synteny and gene content both with one another and with the PInc-2/IncP-2 family of plasmids known to transfer clinically significant drug resistance between <i>Pseudomonas aeruginosa</i> hosts. None of the pQBR plasmids sequenced to date harboured known AMR determinants, but putative phage defence systems and metal resistances were evident. Transposable elements, including the Tn<i>5042</i> mercury resistance transposon, were responsible for significant structural variation within plasmid groups, consistent with a predominant role of transposons in rapidly remodelling plasmids. To experimentally test the ability of pQBR plasmids to spread new traits, we developed a novel transposon transfer assay which showed that certain Group IV pQBR plasmids were especially effective at acquiring the chromosomally encoded transposon Tn<i>6291</i> and that this ability to transfer transposons was likely due to specific plasmid factors rather than generic conjugation rate. Our work presents a tractable set of sequenced plasmids suitable for exploring the evolution and dynamics of gene acquisition by pre-AMR plasmids and provides a key case study highlighting the pervasive interplay between plasmids and transposable elements that can drive microbial genome evolution.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13391042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549442","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":"Benchmarking of real-time, field-deployable whole-genome sequencing of <i>Plasmodium falciparum</i> using Nanopore technology.","authors":"Zahra Razook, Somya Mehra, Myo T Naung, Brittany Gilchrist, Sachintha Wijegunasekara, Digjaya Utama, Dulcie Lautu-Gumal, Abebe A Fola, Didier Menard, James Kazura, Moses Laman, Ivo Mueller, Leanne J Robinson, Melanie Bahlo, Alyssa E Barry","doi":"10.1099/mgen.0.001776","DOIUrl":"10.1099/mgen.0.001776","url":null,"abstract":"<p><p>Malaria parasite genomes have been generated predominantly using Illumina short-read sequencing that requires expensive equipment, is time-consuming with complex protocols, and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with similar data fidelity for single nucleotide variant (SNV) calls compared to standard Illumina whole-genome sequencing. We demonstrate this through sequencing of pure <i>Plasmodium falciparum</i> DNA, mock infections and natural isolates from low-density, asymptomatic infections. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants not detected with short reads. Nanopore genomes can be directly compared to publicly available genomes and produce high-quality end-to-end chromosome assemblies including complex, previously difficult-to-access regions. Nanopore sequencing could expedite whole-genome surveillance of malaria and provide new insights into parasite genome biology.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13435551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148619912","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}