Microbial Genomics最新文献

{"title":"The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.","authors":"Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S Olabode, Alexandru Lepsa, Ana T Duggan, Andrea D Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K Yung, David Bujold, Dusan Andric, Edmund Su, Emma J Griffiths, Gary Van Domselaar, Gordon W Jolly, Heather K E Ward, Henrich Feher, Jared Baker, Jared T Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G Sutcliffe, Susanne A Kraemer, Yelizar Alturmessov, Yann Joly, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Marc Fiume, Terrance P Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G Hussin, Jeffrey B Joy, Caroline Colijn, Paul M K Gordon, William W L Hsiao, Art F Y Poon, Natalie C Knox, Mélanie Courtot, Lincoln Stein, Sarah P Otto, Guillaume Bourque, B Jesse Shapiro, Fiona S L Brinkman","doi":"10.1099/mgen.0.001293","DOIUrl":"https://doi.org/10.1099/mgen.0.001293","url":null,"abstract":"<p><p>The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID-MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11472881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469639","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":"Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from <i>Escherichia coli</i> isolates.","authors":"Gillian Rodger, Samuel Lipworth, Lucinda Barrett, Sarah Oakley, Derrick W Crook, David W Eyre, Nicole Stoesser","doi":"10.1099/mgen.0.001296","DOIUrl":"https://doi.org/10.1099/mgen.0.001296","url":null,"abstract":"<p><p>Whole-transcriptome (long-read) RNA sequencing (Oxford Nanopore Technologies, ONT) holds promise for reference-agnostic analysis of differential gene expression in pathogenic bacteria, including for antimicrobial resistance genes (ARGs). However, direct cDNA ONT sequencing requires large concentrations of polyadenylated mRNA, and amplification protocols may introduce technical bias. Here we evaluated the impact of direct cDNA- and cDNA PCR-based ONT sequencing on transcriptomic analysis of clinical <i>Escherichia coli</i>. Four <i>E. coli</i> bloodstream infection-associated isolates (<i>n</i>=2 biological replicates per isolate) were sequenced using the ONT Direct cDNA Sequencing SQK-DCS109 and PCR-cDNA Barcoding SQK-PCB111.24 kits. Biological and technical replicates were distributed over eight flow cells using 16 barcodes to minimize batch/barcoding bias. Reads were mapped to a transcript reference and transcript abundance was quantified after <i>in silico</i> depletion of low-abundance and rRNA genes. We found there were strong correlations between read counts using both kits and when restricting the analysis to include only ARGs. We highlighted that correlations were weaker for genes with a higher GC content. Read lengths were longer for the direct cDNA kit compared to the PCR-cDNA kit whereas total yield was higher for the PCR-cDNA kit. In this small but methodologically rigorous evaluation of biological and technical replicates of isolates sequenced with the direct cDNA and PCR-cDNA ONT sequencing kits, we demonstrated that PCR-based amplification substantially improves yield with largely unbiased assessment of core gene and ARG expression. However, users of PCR-based kits should be aware of a small risk of technical bias which appears greater for genes with an unusually high (>52%)/low (<44%) GC content.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503500","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":"BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata.","authors":"Linda Fenske, Lukas Jelonek, Alexander Goesmann, Oliver Schwengers","doi":"10.1099/mgen.0.001305","DOIUrl":"10.1099/mgen.0.001305","url":null,"abstract":"<p><p>Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546263","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":"Applying nanopore sequencing technology in <i>Paracoccidioides</i> sp.: a high-quality DNA isolation method for next-generation genomic studies.","authors":"Melina Noelia Lorenzini Campos, Ariel Fernando Amadio, José Matías Irazoqui, Raúl Maximiliano Acevedo, Florencia Dinorah Rojas, Luis Hernando Corredor Sanguña, Laura Belén Formichelli, Raúl Horacio Lucero, Gustavo Emilio Giusiano","doi":"10.1099/mgen.0.001302","DOIUrl":"10.1099/mgen.0.001302","url":null,"abstract":"<p><p>Paracoccidioidomycosis is a severe systemic endemic mycosis caused by <i>Paracoccidioides</i> spp. which mainly affects individuals in Latin America. Progress in <i>Paracoccidioides</i> genomics has been slow, as evidenced by the incomplete reference databases available. Next-generation sequencing is a valuable tool for epidemiological surveillance and genomic characterization. With the ability to sequence long reads without the need for prior amplification, Oxford Nanopore Technology (ONT) offers several advantages, but high-quality and high-quantity DNA samples are required to achieve satisfactory results. Due to the low concentration of <i>Paracoccidioides</i> DNA in clinical samples and inefficient culture isolation methods, DNA extraction can be a significant barrier to genomic studies of this genus. This study proposes a method to obtain a high-coverage <i>de novo</i> genome assembly for <i>Paracoccidioides</i> using an improved DNA extraction method suitable for sequencing with ONT. The assembly obtained was comparable in size to those constructed from available data from Illumina technology. To our knowledge, this is the first genome assembly of <i>Paracoccidioides</i> sp. of such a large size constructed using ONT.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469632","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":"Surveillance of travel-associated isolates elucidates the diversity of non-pandemic <i>Vibrio cholerae</i>.","authors":"Lia Bote, Alyce Taylor-Brown, Mailis Maes, Danielle J Ingle, Mary Valcanis, Benjamin P Howden, Nicholas R Thomson","doi":"10.1099/mgen.0.001307","DOIUrl":"https://doi.org/10.1099/mgen.0.001307","url":null,"abstract":"<p><p><i>Vibrio cholerae</i> is a Gram-negative bacterium found in aquatic environments and is the aetiological agent of cholera, characterized by acute watery diarrhoea and severe dehydration. Cholera presents a significant global health burden of an estimated 1.3-5 million annual cases, with the current pandemic caused by a toxigenic lineage of the O1 El Tor biotype called seventh pandemic El Tor (7PET) that is still ongoing. Whilst it is known that non-7PET lineages can cause sporadic disease, little is known about the transmission of these non-epidemic lineages. Thirty-four <i>V. cholerae</i> isolates were obtained from travellers returning from Indonesia to Australia between 2005 and 2017. These were whole genome sequenced, placed into a global phylogenetic context with 883 isolates, and screened for known genes associated with antimicrobial resistance and virulence. This analysis revealed that 30 isolates fell within non-7PET lineages and four within the 7PET lineage. Both 7PET and non-7PET isolates carried genes for resistance to antibiotics that are commonly used in cholera treatment such as tetracyclines and fluoroquinolones. Diverse virulence factors were also present in non-7PET isolates, with two isolates notably carrying toxin-coregulated pilus genes, which are primarily responsible for intestinal colonization in 7PET <i>V. cholerae</i>. This study demonstrates the role of travel in long-range carriage of epidemic and non-epidemic lineages of <i>V. cholerae,</i> and how sentinel travel surveillance can enrich our knowledge of <i>V. cholerae</i> diversity, reveal new biology about the spread of diverse lineages with differing disease potential and illuminate disease presence in endemic regions with limited surveillance data.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469638","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":"Diversity, functional classification and genotyping of SHV β-lactamases in <i>Klebsiella pneumoniae</i>.","authors":"Kara K Tsang, Margaret M C Lam, Ryan R Wick, Kelly L Wyres, Michael Bachman, Stephen Baker, Katherine Barry, Sylvain Brisse, Susana Campino, Alexandra Chiaverini, Daniela Maria Cirillo, Taane Clark, Jukka Corander, Marta Corbella, Alessandra Cornacchia, Aline Cuénod, Nicola D'Alterio, Federico Di Marco, Pilar Donado-Godoy, Adrian Egli, Refath Farzana, Edward J Feil, Aasmund Fostervold, Claire L Gorrie, Brekhna Hassan, Marit Andrea Klokkhammer Hetland, Le Nguyen Minh Hoa, Le Thi Hoi, Benjamin Howden, Odion O Ikhimiukor, Adam W J Jenney, Håkon Kaspersen, Fahad Khokhar, Thongpan Leangapichart, Małgorzata Ligowska-Marzęta, Iren Høyland Löhr, Scott W Long, Amy J Mathers, Andrew G McArthur, Geetha Nagaraj, Anderson O Oaikhena, Iruka N Okeke, João Perdigão, Hardik Parikh, My H Pham, Francesco Pomilio, Niclas Raffelsberger, Andriniaina Rakotondrasoa, K L Ravi Kumar, Leah W Roberts, Carla Rodrigues, Ørjan Samuelsen, Kirsty Sands, Davide Sassera, Helena Seth-Smith, Varun Shamanna, Norelle L Sherry, Sonia Sia, Anton Spadar, Nicole Stoesser, Marianne Sunde, Arnfinn Sundsfjord, Pham Ngoc Thach, Nicholas R Thomson, Harry A Thorpe, M Estée Torok, Van Dinh Trang, Nguyen Vu Trung, Jay Vornhagen, Timothy Walsh, Ben Warne, Hayley Wilson, Gerard D Wright, Kathryn E Holt, KlebNET-Gsp Amr Genotype-Phenotype Group","doi":"10.1099/mgen.0.001294","DOIUrl":"10.1099/mgen.0.001294","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Interpreting the phenotypes of &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt; alleles in &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt; alleles or additional plasmid-borne &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt; alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases [e.g. the National Center for Biotechnology Information (NCBI) Reference Gene Catalog and the β-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from &lt;i&gt;K. pneumoniae&lt;/i&gt; genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific aa substitutions. We then systematically assigned SHV alleles to functional classes (WT, ESBL and BLI resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with the current assignments in the NCBI's Reference Gene Catalog and/or BLDB (21 to WT, 12 to ESBL and 4 to BLI resistant). Phylogenetic and comparative genomic analyses support that (i) SHV-1 (encoded by &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV-1&lt;/sub&gt;) is the ancestral chromosomal variant, (ii) ESBL- and BLI-resistant variants have evolved multiple times through parallel substitution mutations, (iii) ESBL variants are mostly mobilized to plasmids and (iv) BLI-resistant variants mostly result from mutations in chromosomal &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt;. We used matched genome-phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 &lt;i&gt;K&lt;/i&gt;. &lt;i&gt;pneumoniae&lt;/i&gt; isolates carrying one or more &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt; alleles but no other acquired β-lactamases to assess genotype-phenotype relationships for &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt;. This collection includes human, animal and environmental isolates collected between 2001 and 2021 from 24 countries. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, whilst most omega-loop substitutions do not. Our data also provide support for the WT assignment of 67 protein variants, including 8 that were noted in public databases as ESBL. These eight variants were reclassified as WT because they lack ESBL-associated mutations, and our phenotype data support susceptibility to third-generation cephalosporins (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164 and SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping &lt;i&gt;K. pneumoniae&lt;/i&gt;), whereby known and novel &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;SHV&lt;/sub&gt; alleles are classified b","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469634","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":"Genomics unveils country-to-country transmission between animal hospitals of a multidrug-resistant and sequence type 2 <i>Acinetobacter baumannii</i> clone.","authors":"Amédée André, Julie Plantade, Isabelle Durieux, Pauline Durieu, Anne-Sophie Godeux, Maxence Decellieres, Céline Pouzot-Nevoret, Samuel Venner, Xavier Charpentier, Maria-Halima Laaberki","doi":"10.1099/mgen.0.001292","DOIUrl":"https://doi.org/10.1099/mgen.0.001292","url":null,"abstract":"<p><p><i>Acinetobacter baumannii</i> is a globally distributed opportunistic pathogen in human health settings, including in intensive care units (ICUs). We investigated the contamination of a French small animal ICU with <i>A. baumannii</i>. We discovered repeated animal contamination by <i>A. baumannii</i>, and phylogenetic analysis traced contamination back to a potential foreign animal origin. Genomic analysis combined with antibiotic susceptibility testing revealed heteroresistance to penicillin and aminoglycoside mediated by insertion sequence dynamics and also suggest a potential cross-resistance to human-restricted piperacillin-tazobactam combination. The <i>A. baumannii</i> isolates of the animal ICU belong to the International Clone 2 commonly found in human health settings. Our results suggest a high adaptation of this lineage to healthcare settings and provide questions on the requirements for genetic determinants enabling adaptation to host and abiotic conditions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11472879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469636","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":"Applying rearrangement distances to enable plasmid epidemiology with pling.","authors":"Daria Frolova, Leandro Lima, Leah Wendy Roberts, Leonard Bohnenkämper, Roland Wittler, Jens Stoye, Zamin Iqbal","doi":"10.1099/mgen.0.001300","DOIUrl":"https://doi.org/10.1099/mgen.0.001300","url":null,"abstract":"<p><p>Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological analysis. Typical approaches are either low resolution (replicon typing) or use shared k-mer content to define a genetic distance. However, this distance can both overestimate plasmid relatedness by ignoring rearrangements, and underestimate by over-penalizing gene gain/loss. Therefore a model is needed which captures the key components of how plasmid genomes evolve structurally - through gene/block gain or loss, and rearrangement. A secondary requirement is to prevent promiscuous transposable elements (TEs) leading to over-clustering of unrelated plasmids. We choose the 'Double Cut and Join Indel' (DCJ-Indel) model, in which plasmids are studied at a coarse level, as a sequence of signed integers (representing genes or aligned blocks), and the distance between two plasmids is the minimum number of rearrangement events or indels needed to transform one into the other. We show how this gives much more meaningful distances between plasmids. We introduce a software workflow pling (https://github.com/iqbal-lab-org/pling), which uses the DCJ-Indel model, to calculate distances between plasmids and then cluster them. In our approach, we combine containment distances and DCJ-Indel distances to build a TE-aware plasmid network. We demonstrate superior performance and interpretability to other plasmid clustering tools on the 'Russian Doll' dataset and a hospital transmission dataset.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11472880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469633","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":"Towards quantifying plasmid similarity","authors":"William Matlock, Liam P. Shaw, Samuel K. Sheppard and Edward Feil","doi":"10.1099/mgen.0.001290","DOIUrl":"https://doi.org/10.1099/mgen.0.001290","url":null,"abstract":"Plasmids are extrachromosomal replicons which can quickly spread resistance and virulence genes between clinical pathogens. From the tens of thousands of currently available plasmid sequences we know that overall plasmid diversity is structured, with related plasmids sharing a largely conserved &#8216;backbone&#8217; of genes while being able to carry very different genetic cargo. Moreover, plasmid genomes can be structurally plastic and undergo frequent rearrangements. So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"75 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193191","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":"16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces","authors":"Angelika B. Kiepas, Paul A. Hoskisson and Leighton Pritchard","doi":"10.1099/mgen.0.001287","DOIUrl":"https://doi.org/10.1099/mgen.0.001287","url":null,"abstract":"<span>Streptomyces</span> is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of <span>Streptomyces</span> would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based <span>Streptomyces</span> classifications using 2276 publicly available <span>Streptomyces</span> genome assemblies and 48&#8201;981 publicly available full-length 16S rRNA <span>Streptomyces</span> sequences from <span>silva</span>, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14&#8201;239 distinct <span>Streptomyces</span> sequences that resolves three major lineages of <span>Streptomyces</span>, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for <span>Streptomyces</span>, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate <span>Streptomyces</span> species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as <span>Streptomyces</span> taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the <span>Streptomyces</span> community.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"15 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193262","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}