Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

Wellcome Open Research, Год журнала: 2018, Номер 3, С. 124 - 124

Опубликована: Сен. 24, 2018

The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species genera. Although the PubMLST was conceived as part development first multi-locus typing (MLST) scheme in 1998 software it uses, Bacterial Isolate Genome Sequence database (BIGSdb, published 2010), enables to include all levels data, from single gene sequences up including complete, finished genomes. Here we describe developments BIGSdb made publication June 2018 show how platform realises genomics wide range applications. system is based on gene-by-gene analysis genomes, each deposited annotated identify genes present systematically catalogue their variation. Originally intended means characterising isolates schemes, synthesis records genetic variation permits highly scalable (whole genome tens thousands isolates) addressing functional questions, including: prediction antimicrobial resistance; likely cross-reactivity vaccine antigens; activities variants lead key phenotypes. There are no limitations number sequences, loci, allelic or schemes (combinations loci) can be included, enabling represent an expanding question. In addition providing web-accessible analyses links third-party visualisation tools, includes RESTful application programming interface (API) access underlying applications pipelines.

Язык: Английский

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ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

PLoS Computational Biology, Год журнала: 2015, Номер 11(2), С. e1004041 - e1004041

Опубликована: Фев. 12, 2015

Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference simultaneously detect recombination bacterial genomes and account for phylogenetic reconstruction. ClonalFrameML can analyse hundreds matter hours, demonstrate its usefulness on simulated real datasets. We find evidence hotspots associated with mobile elements Clostridium difficile ST6 previously undescribed 310kb chromosomal replacement Staphylococcus aureus ST582. freely available at http://clonalframeml.googlecode.com/.

Язык: Английский

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The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Genome Research, Год журнала: 2019, Номер 30(1), С. 138 - 152

Опубликована: Дек. 6, 2019

EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera include pathogens. Here, we provide overview how works, what it can do, and its future prospects. has currently assembled more than 300,000 genomes from Illumina short reads

Язык: Английский

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GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Genome Research, Год журнала: 2018, Номер 28(9), С. 1395 - 1404

Опубликована: Июль 26, 2018

Current methods struggle to reconstruct and visualize the genomic relationships of large numbers bacterial genomes. GrapeTree facilitates analyses allelic profiles by a static “GrapeTree Layout” algorithm that supports interactive visualizations trees within web browser window. also implements novel minimum spanning tree (MSTree V2) genetic despite high levels missing data. is stand-alone package for investigating phylogenetic plus associated metadata integrated into EnteroBase facilitate cutting edge navigation among pathogens.

Язык: Английский

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MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Microbial Genomics, Год журнала: 2018, Номер 4(8)

Опубликована: Июль 27, 2018

Large-scale bacterial population genetics studies are now routine due to cost-effective Illumina short-read sequencing. However, analysing plasmid content remains difficult incomplete assembly of plasmids. Bacterial isolates can contain any number plasmids and complicated the presence repetitive elements. Numerous tools have been developed analyse but performance functionality variable. The MOB-suite was as a set modular for reconstruction typing from draft data facilitate characterization Using closed genomes with publicly available data, identified contigs origin both high sensitivity specificity (95 88 %, respectively). In comparison, plasmidfinder demonstrated (99 %) limited (50 %). same dataset 377 known plasmids, MOB-recon accurately reconstructed 207 so that they were assigned single grouping without other or chromosomal sequences, whereas plasmidSPAdes only able reconstruct 102 general, has tendency merge different together, 208 undergoing events. reduces errors produces more hybrid 84 splits merges. also provides replicon similar inclusion relaxase prediction conjugation potential. is written in Python 3 https://github.com/phac-nml/mob-suite.

Язык: Английский

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Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

Nature Microbiology, Год журнала: 2016, Номер 2(2)

Опубликована: Окт. 10, 2016

Язык: Английский

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A genomic overview of the population structure of Salmonella

PLoS Genetics, Год журнала: 2018, Номер 14(4), С. e1007261 - e1007261

Опубликована: Апрель 5, 2018

For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further for epidemiological tracing a variety of diagnostic tests with higher resolution. Recently, it proposed that so-called eBurst groups (eBGs) based on the alleles seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks resolution needed existence had not independently validated independent criteria. Here, we describe EnteroBase, web-based platform assembles draft genomes from Illumina short reads in public domain are uploaded users. EnteroBase implements legacy MLST as well ribosomal gene (rMLST), core genome (cgMLST), whole (wgMLST) currently contains over 100,000 assembled Salmonella. It also provides graphical tools visual interrogation these genotypes those single nucleotide polymorphisms (SNPs). eBGs largely consistent rMLST, thus demonstrating correspond populations. rMLST facilitated selection representative SNP analyses entire breadth diversity within In contrast, cgMLST investigations. These observations show genomic genotyping, assistance can be applied at all levels genus.

Язык: Английский

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The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

PLoS ONE, Год журнала: 2016, Номер 11(1), С. e0147101 - e0147101

Опубликована: Янв. 22, 2016

For nearly 100 years serotyping has been the gold standard for identification of Salmonella serovars. Despite increasing adoption DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing burden salmonellosis. At same time, recent advances whole-genome sequencing (WGS) promise to revolutionize our ability perform advanced pathogen characterization support improved source attribution outbreak analysis. We present In Silico Typing Resource (SISTR), bioinformatics platform rapidly performing simultaneous silico analyses several leading methods on draft genome assemblies. addition serovar prediction by genoserotyping, this resource integrates sequence-based typing for: Multi-Locus Sequence (MLST), ribosomal MLST (rMLST), core (cgMLST). show how phylogenetic context from cgMLST analysis can supplement genoserotyping increase accuracy over 94.6% dataset comprised 4,188 finished genomes WGS allowing user-uploaded assemblies, SISTR incorporates database comprising 4,000 publicly available genomes, users place their isolates broader epidemiological context. The metadata driven visualizations examine phylogenetic, geospatial temporal distribution genome-sequenced isolates. As laboratories around world becomes increasingly common, rapid minimally processed assemblies provides powerful approach molecular epidemiology investigations. Moreover, type integrated using multiple sub-typing allows continuity with historical data as we transition towards genomic epidemiology. is freely web https://lfz.corefacility.ca/sistr-app/.

Язык: Английский

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Application of next generation sequencing in clinical microbiology and infection prevention

Journal of Biotechnology, Год журнала: 2016, Номер 243, С. 16 - 24

Опубликована: Дек. 29, 2016

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence a complete bacterial genome in single run, from these data, on resistance virulence, as well typing obtained, useful The obtained data can be further used development an outbreak-specific screening test. In this review, general introduction to NGS presented, including library preparation major characteristics most common platforms, such MiSeq (Illumina) Ion PGM™ (ThermoFisher). An overview software analyses at medical microbiology diagnostic laboratory University Medical Center Groningen Netherlands given. Furthermore, applications clinical setting are described, management, case finding, characterization surveillance pathogens, rapid identification bacteria using 16S-23S rRNA region, taxonomy, metagenomics approaches samples, determination zoonotic micro-organisms animals humans. Finally, we share our vision use personalised near future, pointing out specific requirements.

Язык: Английский

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The population genetics of pathogenic Escherichia coli

Nature Reviews Microbiology, Год журнала: 2020, Номер 19(1), С. 37 - 54

Опубликована: Авг. 21, 2020

Язык: Английский

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