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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Book ChapterDOI
Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications. Methods, Analyses, and Applications.
Marcos Pérez-Losada,Marcos Pérez-Losada,Marcos Pérez-Losada,Miguel Arenas,Eduardo Castro-Nallar +4 more
TL;DR: This work states that the increasing speed, quantity and quality, and reduced cost of gene and genome nucleotide sequencing, together with improved web-based databases, analytical tools, and rising computer power, will lead to a continued expansion in the use of MLST and its integration with cost-effective pathogen genome sequencing.
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Proteus columbae sp. nov., isolated from a pigeon in Ma'anshan, China.
TL;DR: A Gram-negative, facultatively anaerobic bacillus isolated from the flesh of a pigeon specimen collected in Ma'anshan, Anhui province, China, represents a novel species of the genus Proteus, for which the nameproteuscolumbae sp.
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Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal.
Célia Leão,Lurdes Clemente,Laura Moura,Anne Mette Seyfarth,Inge M Hansen,Rene S. Hendriksen,Ana L. Amaro +6 more
TL;DR: Four Escherichia coli strains harboring the blaCTX–M–65 gene identified among 49 isolates from beef and pork collected at retail are characterized by whole-genome sequencing and showed that they are clonally related and belong to two sub-lineages.
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Safety demonstration of a microbial species for use in the food chain: Weissella confusa.
TL;DR: The phenotypic study, genomic characterization and bibliographical survey will allow us to conclude about the safety of the species and confirm its use for food fermentation and consider specific strains for demonstration of their respective health effects as probiotic candidates.
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Transmissible silver resistance readily evolves in high-risk clone isolates of Klebsiella pneumoniae.
TL;DR: The results show that multidrug-resistant high-risk clones of K. pneumoniae are capable of evolving and transmitting high-level resistance to silver and the lack of fitness cost associated with the carriage of the CHASRI in a silver-free environment and the presence of the RelEB toxin-antitoxin system on the conjugative plasmids could advance the dissemination of silver resistance.
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