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
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Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates.
Sara Lomonaco,Matthew A. Crawford,Christine Lascols,Ruth Timme,Kevin Anderson,David R. Hodge,Debra J. Fisher,Segaran P. Pillai,Stephen A. Morse,Erum Khan,Molly A. Hughes,Marc W. Allard,Shashi Sharma +12 more
TL;DR: WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan to provide a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.
Journal ArticleDOI
Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases.
Peter Gerner-Smidt,John M. Besser,Jeniffer Concepción-Acevedo,Jason P. Folster,Jasmine Huffman,Lavin A. Joseph,Zuzana Kucerova,Megin Nichols,Colin Schwensohn,Beth Tolar +9 more
TL;DR: Using recent examples from outbreaks investigated in the United States, some aspects of One Health approaches that have been used successfully to solve such outbreaks are presented, including using different combinations of flexible WGS based case definition, efficient epidemiological follow-up, traceback, surveillance and testing of potential food and environmental sources and animal hosts.
Journal ArticleDOI
Multihospital Occurrence of Pan-Resistant Klebsiella pneumoniae Sequence Type 147 with an ISEcp1-Directed blaOXA-181 Insertion in the mgrB Gene in the United Arab Emirates.
Agnes Sonnevend,Akela Ghazawi,Rayhan Hashmey,Aliasgher Haidermota,Safinaz Girgis,Mubarak Alfaresi,Mohammed Omar,David L. Paterson,David L. Paterson,Hosam M. Zowawi,Tibor Pál +10 more
TL;DR: A cluster of 9 pan-resistant K. pneumoniae sequence type 147 (ST147) isolates encountered in 4 patients over nearly 1 year in 3 hospitals of the United Arab Emirates show that this pan- resistant clone has an alarming capacity to maintain itself over an extended period of time and is even likely to be transmitted internationally.
Journal ArticleDOI
Global Molecular Epidemiology of IMP-Producing Enterobacteriaceae
Yasufumi Matsumura,Yasufumi Matsumura,Gisele Peirano,Mary Motyl,Mark Raymond Adams,Liang Chen,Barry N. Kreiswirth,Rebekah DeVinney,Johann D. D. Pitout +8 more
TL;DR: The importance of surveillance programs using the latest molecular techniques for providing insight into the characteristics and global distribution of Enterobacteriaceae with blaIMP genes is highlighted.
Journal ArticleDOI
Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase-48-Like Carbapenemases, United States.
Joseph D. Lutgring,Wenming Zhu,Tom J. B. de Man,Johannetsy J. Avillan,Karen Anderson,David Lonsway,Lori A. Rowe,Dhwani Batra,J. Kamile Rasheed,Brandi Limbago +9 more
TL;DR: P phenotypic and genotypic characterization of 30 Enterobacteriaceae producing OXA-48–like carbapenemases that were recovered from patients during 2010–2014 found all isolates were resistant to ertapenems and showed positive results for the ertAPenem and meropenem modified Hodge test and the modified carbapanem inactivation method.
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.