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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Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam
Samuel J. Bloomfield,Vu Thuy Duong,Ha Thanh Tuyen,James Campbell,Nicholas R. Thomson,Julian Parkhill,Hoang Le Phuc,Tran Thi Hong Chau,Duncan J. Maskell,Gabriel G. Perron,Nguyen Minh Ngoc,Lu Lan Vi,Evelien M. Adriaenssens,Stephen Baker,Alison E. Mather +14 more
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Occurrence and Characteristics of Mcrs among Gram-Negative Bacteria Causing Bloodstream Infections of Infant Inpatients between 2006 and 2019 in China
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Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils.
Rosalba Salgado-Morales,Nancy Rivera-Gómez,Fernando Martínez-Ocampo,Luis Fernando Lozano-Aguirre Beltrán,Armando Hernández-Mendoza,Edgar Dantán-González +5 more
TL;DR: The draft genome sequence of Photorhabdus luminescens strain HIM3, a symbiotic bacterium associated with the entomopathogenic nematode Heterorhabditis indica MOR03, isolated from soil sugarcane in Yautepec, Morelos, Mexico, is reported.
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Penicillin resistance in bovine Staphylococcus aureus: Genomic evaluation of the discrepancy between phenotypic and molecular test methods.
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Horsing around: Escherichia coli ST1250 of equine origin harbouring epidemic IncHI1/ST9 plasmid with blaCTX-M-1 and an operon for short-chain fructooligosaccharides metabolism.
Adam Valcek,Petra Sismova,Kristina Nesporova,Søren Overballe-Petersen,Ibrahim Bitar,Ivana Jamborova,Arie Kant,Jaroslav Hrabak,Jaap A. Wagenaar,Jean Yves Madec,Peter Damborg,Engeline van Duijkeren,Christa Ewers,Joost Hordijk,Henrik Hasman,Michael S.M. Brouwer,Monika Dolejska +16 more
TL;DR: The relatedness of the equine-associated Escherichia coli strain ST1250 and its single and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis as mentioned in this paper.
References
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