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
Citations
More filters
Journal ArticleDOI
Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine.
Li Chen,Leyi Wang,Afrah Kamal Yassin,Afrah Kamal Yassin,Jilei Zhang,Jiansen Gong,Kezong Qi,Roman R. Ganta,Yuanyuan Zhang,Yi Yang,Xiangan Han,Chengming Wang +11 more
TL;DR: Comparative genomic analyses of the 19 diverse E. coli isolates provided insights into molecular basis of the rising multi-drug resistance in E. Escherichia coli.
Posted ContentDOI
Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli
Rafael Patiño-Navarrete,Isabelle Rosinski-Chupin,Nicolas Cabanel,Lauraine Gauthier,Julie Takissian,Jean-Yves Madec,Monzer Hamze,Rémy A. Bonnin,Thierry Naas,Philippe Glaser,Philippe Glaser +10 more
TL;DR: It is shown that the fixation of carbapenemase genes depends largely on a combination of mutations in ftsI encoding the penicillin binding protein 3 and in the porin genes ompC and ompF, which spread across the species by recombination.
Journal ArticleDOI
OUP accepted manuscript
TL;DR: Zhang et al. as discussed by the authors proposed VRprofile2, an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences, which can aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure.
Journal ArticleDOI
Hospital outbreak caused by linezolid resistant Enterococcus faecium in Upper Austria.
Heidrun Kerschner,Adriana Cabal,Rainer Hartl,Sigrid Machherndl-Spandl,Franz Allerberger,Werner Ruppitsch,Petra Apfalter +6 more
TL;DR: WGS proved to be an effective tool to differentiate several LREfm clusters in an outbreak and is important in a high-risk setting such as hematooncology, where multiple introductions are possible and occur despite intensified infection control measures.
Journal ArticleDOI
Field investigations of multidrug-resistant Salmonella Infantis epidemic strain incursions into broiler flocks in England and Wales.
TL;DR: The study shows that to remove S. Infantis from premises effectively, a combined approach to poultry houses and the surrounding farm environment is necessary and a revised cleaning and disinfection programme was developed that was associated with the clearance of MDR S.Infantis.
References
More filters
Journal ArticleDOI
Identification of acquired antimicrobial resistance genes
Ea Zankari,Henrik Hasman,Salvatore Cosentino,Martin Vestergaard,Simon Rasmussen,Ole Lund,Frank Møller Aarestrup,Mette Voldby Larsen +7 more
TL;DR: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created, and the method was evaluated on WGS chromosomes and plasmids of 30 isolates.
Journal ArticleDOI
CDD: a Conserved Domain Database for the functional annotation of proteins
Aron Marchler-Bauer,Shennan Lu,John B. Anderson,Farideh Chitsaz,Myra K. Derbyshire,Carol DeWeese-Scott,Jessica H. Fong,Lewis Y. Geer,Renata C. Geer,Noreen R. Gonzales,Marc Gwadz,David I. Hurwitz,John D. Jackson,Zhaoxi Ke,Christopher J. Lanczycki,Fu-Ping Lu,Gabriele H. Marchler,Mikhail Mullokandov,Marina V. Omelchenko,Cynthia L. Robertson,James S. Song,Narmada Thanki,Roxanne A. Yamashita,Dachuan Zhang,Naigong Zhang,Chanjuan Zheng,Stephen H. Bryant +26 more
TL;DR: NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints.
Journal ArticleDOI
Identification of plasmids by PCR-based replicon typing
Alessandra Carattoli,Alessia Bertini,Laura Villa,Vincenzo Falbo,Katie L. Hopkins,E. John Threlfall +5 more
TL;DR: Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmid in epidemiologically unrelated Salmonella isolates of different serotypes.
Journal ArticleDOI
BIGSdb: Scalable analysis of bacterial genome variation at the population level
TL;DR: The Bacterial Isolate Genome Sequence Database (BIGSDB) represents a freely available resource that will assist the broader community in the elucidation of the structure and function of bacteria by means of a population genomics approach.
Journal ArticleDOI
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette Voldby Larsen,Salvatore Cosentino,Simon Rasmussen,Carsten Friis,Henrik Hasman,Rasmus L. Marvig,Lars Jelsbak,Thomas Sicheritz-Pontén,David W. Ussery,Frank Møller Aarestrup,Ole Lund +10 more
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.