The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria : report from the EUCAST Subcommittee
Matthew J. Ellington,Oskar Ekelund,Frank Møller Aarestrup,Rafael Cantón,Michel Doumith,Christian G. Giske,H. Grundman,Henrik Hasman,Matthew T. G. Holden,Katie L. Hopkins,J. Iredell,Gunnar Kahlmeter,Claudio U. Köser,Alasdair P. MacGowan,Dik Mevius,Dik Mevius,Michael R. Mulvey,Thierry Naas,Tim E. A. Peto,J.-M. Rolain,Ørjan Samuelsen,Neil Woodford +21 more
TLDR
The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of Whole Genome Sequencing (WGS) for bacterial antimicrobial susceptibility testing (AST) as discussed by the authors.About:
This article is published in Clinical Microbiology and Infection.The article was published on 2017-01-01 and is currently open access. It has received 346 citations till now.read more
Citations
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ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia,Rolf Sommer Kaas,Etienne Ruppé,Marilyn C. Roberts,Stefan Schwarz,Vincent Cattoir,Alain Philippon,Rosa Lundbye Allesøe,Rosa Lundbye Allesøe,Ana-Rita Rebelo,Alfred Ferrer Florensa,Linda Fagelhauer,Trinad Chakraborty,Bernd Neumann,Guido Werner,Jennifer K. Bender,Kerstin Stingl,Minh Ngoc Nguyen,Jasmine Coppens,Basil Britto Xavier,Surbhi Malhotra-Kumar,Henrik Westh,Henrik Westh,Mette Pinholt,Muna F. Anjum,Nicholas A. Duggett,Isabelle Kempf,Suvi Nykäsenoja,Satu Olkkola,Kinga Wieczorek,Ana Amaro,Lurdes Clemente,Joël Mossong,Serge Losch,Catherine Ragimbeau,Ole Lund,Frank Møller Aarestrup +36 more
TL;DR: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
Journal ArticleDOI
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
TL;DR: This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations.
Journal ArticleDOI
Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases.
TL;DR: With the development of mNGS assays, it is essential for treating practitioners to understand both the power and limitations of the method as a diagnostic tool.
Journal ArticleDOI
Methods for the detection and identification of pathogenic bacteria: past, present, and future
Linda Váradi,Linda Váradi,Jia Lin Luo,David E. Hibbs,John D. Perry,Rosaleen J. Anderson,Sylvain Orenga,Paul W. Groundwater +7 more
TL;DR: The challenges associated with the detection and identification of pathogenic bacteria are highlighted, by providing an introduction to the techniques currently used, as well as newer techniques that are in development.
Journal ArticleDOI
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis
Scott Quainoo,Jordy P. M. Coolen,Sacha A. F. T. van Hijum,Martijn A. Huynen,Willem J. G. Melchers,Willem van Schaik,Heiman F. L. Wertheim +6 more
TL;DR: This review assesses the feasibility of whole-genome sequencing (WGS) technologies and bioinformatics analysis tools for nosocomial outbreak analyses, and presents a real-world example of the implementation of WGS for antimicrobial resistance analysis.
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
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: A microbiological and molecular biological study
Yiyun Liu,Yang Wang,Timothy R. Walsh,Ling-Xian Yi,Rong Zhang,James Spencer,Yohei Doi,Guo-Bao Tian,Baolei Dong,Xianhui Huang,Lin-Feng Yu,Danxia Gu,Hongwei Ren,Xiaojie Chen,Luchao Lv,Dandan He,Hongwei Zhou,Zi-sen Liang,Jian-Hua Liu,Jianzhong Shen +19 more
TL;DR: The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance, in Enterobacteriaceae and emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.
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Acinetobacter baumannii: Emergence of a Successful Pathogen
TL;DR: This review details the significant advances that have been made in understanding of this remarkable organism over the last 10 years, including current taxonomy and species identification, issues with susceptibility testing, mechanisms of antibiotic resistance, global epidemiology, clinical impact of infection, host-pathogen interactions, and infection control and therapeutic considerations.
Journal ArticleDOI
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
TL;DR: 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.
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Antibacterial-Resistant Pseudomonas aeruginosa: Clinical Impact and Complex Regulation of Chromosomally Encoded Resistance Mechanisms
TL;DR: This review highlights the clinical significance of chromosomally encoded AmpC cephalosporinase, the outer membrane porin OprD, and the multidrug efflux pumps, as well as the complex mechanisms/pathways by which P. aeruginosa regulates their expression.
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