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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The clinical and microbiological characteristics of enteric fever in Cambodia, 2008-2015.
Laura Maria Francisca Kuijpers,Laura Maria Francisca Kuijpers,Thong Phe,Chhun Heng Veng,Kruy Lim,Sovann Ieng,Chun Kham,Nizar Fawal,Laetitia Fabre,Simon Le Hello,Erika Vlieghe,François-Xavier Weill,Jan Jacobs,Jan Jacobs,Willy Peetermans +14 more
TL;DR: In Phnom Penh, Cambodia, Salmonella Paratyphi A now causes the majority of enteric fever cases and decreased susceptibility against ciprofloxacin is increasing andSalmonella Typhi was significantly more associated with MDR and DCS compared to Salmonello ParatYphi A.
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Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon.
Luria Leslie Founou,Raspail Carrel Founou,Mushal Allam,Arshad Ismail,Cyrille F. Djoko,Sabiha Y. Essack +5 more
TL;DR: This study shows that ESBL-producing K. pneumoniae is actively disseminating in pigs and occupationally exposed workers in Cameroonian pig abattoirs and is probably underestimated in the absence of molecular epidemiological studies, which underline the existence of a potential unheeded food safety and public health threat associated with these resistant strains.
Journal ArticleDOI
Plasmid-Mediated Transmission of KPC-2 Carbapenemase in Enterobacteriaceae in Critically Ill Patients.
Christian Schweizer,Peter Bischoff,Jennifer K. Bender,Axel Kola,Petra Gastmeier,Manfred Hummel,Frank-Rainer Klefisch,Felix Schoenrath,Andre Frühauf,Yvonne Pfeifer +9 more
TL;DR: An outbreak of KPC-2-producing CRE that was caused by horizontal transmission of a promiscuous plasmid across different genera of bacteria and hospitals in Germany is reported and data suggest a regional and supraregional spread of blaKPC- 2-carrying IncN-plasmids harboring the Tn4401g isoform in Germany.
Journal ArticleDOI
Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways.
James P. J. Hall,James P. J. Hall,James P. J. Hall,Rosanna C. T. Wright,David Guymer,Ellie Harrison,Michael A. Brockhurst +6 more
TL;DR: Plasmid compensatory evolution is fast enough to allow survival of a plasmid despite it imposing very high fitness costs upon its host, and indeed may regularly occur during the process of isolating and selecting individual plasmids-containing clones.
Journal ArticleDOI
Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.
Kotaro Aoki,Sohei Harada,Sohei Harada,Koji Yahara,Yoshikazu Ishii,Daisuke Motooka,Shota Nakamura,Yukihiro Akeda,Tetsuya Iida,Kazunori Tomono,Satoshi Iwata,Kyoji Moriya,Kazuhiro Tateda +12 more
TL;DR: Observations suggest that IMP-producing E. cloacae complex isolates with a diversity of host genomic backgrounds have spread in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids toward this phenomenon.
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.