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
Citations
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Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.
Matt Bawn,Nabil-Fareed Alikhan,Gaetan Thilliez,Mark Kirkwood,Nicole E. Wheeler,Liljana Petrovska,Timothy J. Dallman,Evelien M. Adriaenssens,Neil Hall,Robert A. Kingsley,Robert A. Kingsley +10 more
TL;DR: The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroups of ST36, which were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition ofClade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes.
Journal ArticleDOI
Molecular Diversity and Plasmid Analysis of KPC-Producing Escherichia coli
TL;DR: Overall, this study shows that the spread of blaKPC-producing E. coli is largely due to horizontal transfer of bloKNPC-harboring plasmids and related mobile elements into diverse genetic backgrounds, demonstrating the plasticity of these plasmid and their rapid evolution in the clinic.
Journal ArticleDOI
Annotation of plasmid genes.
Christopher M. Thomas,Nicholas R. Thomson,Ana Cerdeño-Tárraga,Celeste J. Brown,Eva M. Top,Laura S. Frost +5 more
TL;DR: This short review highlights some of the current issues and suggests some ways forward in annotation of plasmid genomes and recommends that annotators use a whole system naming approach.
Journal ArticleDOI
Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil.
Marisa Fabiana Nicolás,Pablo Ivan Pereira Ramos,Fabíola Marques de Carvalho,Dhian R A Camargo,Carlene de Fátima Morais Alves,Guilherme Loss de Morais,Luiz Gonzaga Paula de Almeida,Rangel C. Souza,Luciane Prioli Ciapina,Ana Carolina Paulo Vicente,Roney S. Coimbra,Ana Tereza Ribeiro de Vasconcelos +11 more
TL;DR: The first complete genome reported to date of a clinical isolate of this subspecies harboring both class A beta-lactamases KPC-2 and OKP-B-6 from South America is presented and contributes to the description of the characteristics of a novel K. similip pneumoniae strain circulating in South America that currently represent a serious potential risk for nosocomial settings.
Journal ArticleDOI
Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms.
Andrea Garretto,Taylor Miller-Ensminger,Adriana Ene,Zubia Merchant,Aashaka C. Shah,Athina Gerodias,Anthony Biancofiori,Stacey Canchola,Stephanie Canchola,Emanuel Castillo,Tasnim Chowdhury,Nikita Gandhi,Sarah Hamilton,Kyla Hatton,Syed Hyder,Koty Krull,Demetrios Lagios,Thinh Lam,Kennedy Mitchell,Christine Mortensen,Amber Murphy,Joseph Richburg,Meghan Rokas,Suzanne Ryclik,Pauline Sulit,Thomas Szwajnos,Manuel Widuch,Jessica Willis,Mary Woloszyn,Bridget Brassil,Genevieve Johnson,Rita Mormando,Laura Maskeri,Mary Batrich,Nicole Stark,Jason W. Shapiro,Cesar Montelongo Hernandez,Swarnali Banerjee,Alan J. Wolfe,Catherine Putonti +39 more
TL;DR: It is hypothesized that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition, rather than the presence of the virus itself, as previously found.
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