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
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Journal ArticleDOI
Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca.
Adelumola Oladeinde,Kimberly L. Cook,Steven M. Lakin,Reed Woyda,Zaid Abdo,Torey Looft,Kyler Herrington,Gregory Zock,Jodie Plumblee Lawrence,Jesse C. Thomas,Megan S. Beaudry,Travis C. Glenn +11 more
TL;DR: In this paper, the authors used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg.
Journal ArticleDOI
Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin
Apostolos Liakopoulos,Jeanet van der Goot,Alex Bossers,Jonathan W. Betts,Michael S.M. Brouwer,Arie Kant,Hilde E. Smith,Daniela Ceccarelli,Dik Mevius +8 more
TL;DR: The findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host, and might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands.
Journal ArticleDOI
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level.
Guilhem Royer,Guilhem Royer,Guilhem Royer,J. W. Decousser,J. W. Decousser,Catherine Branger,Mathieu Dubois,Claudine Médigue,Erick Denamur,David Vallenet +9 more
TL;DR: Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus, and a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level is developed.
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Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of blaTEM-1B.
Alasdair T. M. Hubbard,Jenifer Mason,Paul Roberts,Paul Roberts,Christopher M. Parry,Caroline E Corless,Jon van Aartsen,Alex Howard,Issra Bulgasim,Alice J. Fraser,Emily R. Adams,Adam P. Roberts,Thomas Edwards +12 more
TL;DR: A mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B is reported, leading to TEM- 1B hyperproduction and TZP resistance.
Journal ArticleDOI
Whole genome sequencing for the molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains isolated at the Italian ASST Fatebenefratelli Sacco Hospital, 2012-2014.
Sara Giordana Rimoldi,Bernardina Gentile,Cristina Pagani,Annamaria Di Gregorio,Anna Anselmo,Anna Maria Palozzi,Antonella Fortunato,Valentina Pittiglio,Anna Lisa Ridolfo,Maria Rita Gismondo,Giuliano Rizzardini,Florigio Lista +11 more
TL;DR: The findings support the importance of implementing bacterial genomics in clinical medicine in order to complement traditional methods and overcome their limited resolution.
References
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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.