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
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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Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa
Mauro M.S. Saraiva,Valdinete Pereira Benevides,N. M. V. Silva,Alessandro M. Varani,Oliveiro Caetano de Freitas Neto,A. Berchieri,Enrique Jesús Delgado-Suárez,Alan Douglas de Lima Rocha,Tadesse Eguale,Janet A. Munyalo,Samuel Kariuki,Wondwossen A. Gebreyes,Celso José Bruno de Oliveira +12 more
TL;DR: In this article , the antimicrobial resistance profile and genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19) were investigated through phylogenetic and pangenome analyses.
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High-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period
Gizem Levent,Ashlynn Schlochtermeier,Samuel E. Ives,Keri N. Norman,Sara D. Lawhon,Guy H. Loneragan,Robin C. Anderson,Javier Vinasco,H. C. den Bakker,Harvey Morgan Scott +9 more
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TL;DR: Wang et al. as mentioned in this paper reported the prevalence of mcr-1 among clinical infected Salmonella isolates in China, but the transmission dynamics of mCR-1 in different ecological niches were not well investigated.
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