In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli,Ea Zankari,Aurora García-Fernández,Mette Voldby Larsen,Ole Lund,Laura Villa,Frank Møller Aarestrup,Henrik Hasman +7 more
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TLDR
Two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae are designed and developed.Abstract:
In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S . Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.read more
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PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets.
TL;DR: PlasForest as mentioned in this paper is a homology-based random forest classifier that identifies bacterial plasmid sequences in partially assembled genomes without knowing the taxonomical origin of the samples, it can detect contigs as plasmids or chromosomes with a F1 score of 0.950.
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Implications of stx loss for clinical diagnostics of Shiga toxin-producing Escherichia coli.
Thulasika Senthakumaran,Thulasika Senthakumaran,Lin Torstensen Brandal,Bjørn-Arne Lindstedt,Silje Bakken Jørgensen,Colin Charnock,Hege Smith Tunsjø,Hege Smith Tunsjø +7 more
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A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
Shady Mansour Kamal,Shady Mansour Kamal,Annika Cimdins‐Ahne,Changhan Lee,Fengyang Li,Alberto J. Martín-Rodríguez,Zaira Seferbekova,Robert Afasizhev,Haleluya Wami,Panagiotis Katikaridis,Lena Meins,Heinrich Lünsdorf,Ulrich Dobrindt,Axel Mogk,Ute Römling +14 more
TL;DR: A unique contribution of ClpGGI‐Fec10 to the exquisite thermotolerance of E. coli Fec10 is noted, suggesting functional differences between both disaggregases in vivo, and hints to the successful establishment of food‐borne heat‐resistant strains in the human gut.
References
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