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
Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins
TL;DR: The plasmid typing system developed for A. baumannii plasmids with an identifiable rep gene will facilitate the classification and tracking of sequenced plasmIDS and enable the detection of plasmID-derived contigs present in draft genomes that are widely ignored currently.
Journal ArticleDOI
Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana.
Lauren K. Hudson,Lisha Constantine-Renna,Linda Thomas,Christina Moore,Xiaorong Qian,Katie Garman,John R. Dunn,Thomas G. Denes +7 more
TL;DR: The population structure of TN and global Salmonella ser.
Journal ArticleDOI
Emergence of Cfr-Mediated Linezolid Resistance among Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) from Healthy Pigs in Portugal
TL;DR:
Journal ArticleDOI
Flanker: a tool for comparative genomics of gene flanking regions.
William Matlock,Samuel Lipworth,Bede Constantinides,Tim E. A. Peto,A. Sarah Walker,Derrick W. Crook,Susan R. Hopkins,Liam P. Shaw,Nicole Stoesser +8 more
TL;DR: Flanker as discussed by the authors is a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure.
Journal ArticleDOI
Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources
TL;DR: This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBLs, and identifies the ST131-C1-M27 clade gaining prevalence in Europe.
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.