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
Citations
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High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings
Maria Camila Montealegre,Alba Talavera Rodríguez,Subarna Roy,Muhammed Iqbal Hossain,Mohammad Aminul Islam,Mohammad Aminul Islam,Val F. Lanza,Timothy R. Julian,Timothy R. Julian,Timothy R. Julian +9 more
TL;DR: Interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.
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Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity
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TL;DR: In this article, the authors found that antibiotic resistant Klebsiella pneumoniae is a leading public health threat and gastrointestinal carriage is an established risk factor for subsequent infections during hospitalization.
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Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch
Silvia Argimon,Sophia David,Anthony Underwood,Monica Abrudan,Nicole E. Wheeler,Mihir Kekre,Khalil Abudahab,Corin A. Yeats,Richard Goater,Ben Taylor,Harry Harste,Dawn Muddyman,Edward J. Feil,Sylvain Brisse,Kathryn E. Holt,Pilar Donado-Godoy,K L Ravikumar,Iruka N. Okeke,Celia C. Carlos,David M. Aanensen +19 more
TL;DR: Pathogenwatch as mentioned in this paper is a free web application for analysis of Klebsiella genomes to aid surveillance at local, national and global levels, which can identify hospital outbreaks, detect introductions from abroad, and uncover clonal expansions associated with resistance and virulence genes.
Journal ArticleDOI
Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal
Vera Manageiro,Daniel A. Sampaio,Patrícia Mendes Pereira,Paulo César de Matos Rodrigues,Luís Vieira,Carlos Palos,Manuela Caniça +6 more
TL;DR: The draft genome sequence of the first NDM-1-producing Providencia stuartii strain isolated in Portugal revealed the presence of an incompatibility group A/C2 (IncA/C1) plasmid and of diverse acquired genes conferring resistance to β-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides.
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Genomic Dissection of Travel-Associated Extended-Spectrum-Beta-Lactamase-Producing Salmonella enterica Serovar Typhi Isolates Originating from the Philippines: a One-Off Occurrence or a Threat to Effective Treatment of Typhoid Fever?
Rene S. Hendriksen,Pimlapas Leekitcharoenphon,Matthew Mikoleit,Jacob Dyring Jensen,Rolf Sommer Kaas,Louise Roer,Heena B. Joshi,Srirat Pornruangmong,Chaiwat Pulsrikarn,Gladys D. Gonzalez-Aviles,E. Ascelijn Reuland,Nashwan al Naiemi,Astrid Louise Wester,Frank Møller Aarestrup,Henrik Hasman +14 more
TL;DR: One unreported case of extended-spectrum-beta-lactamase (ESBL)-producing Salmonella enterica serovar Typhi was identified and whole-genome sequence typed, among other analyses, and compared to other available genomes of S. Typhi.
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