Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data.
Nicole Stoesser,Elizabeth M. Batty,David W Eyre,Marcus Morgan,David H. Wyllie,C del Ojo Elias,James R. Johnson,A S Walker,Tim E. A. Peto,Derrick W. Crook +9 more
TLDR
The whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae was as sensitive and specific as routinely deployed phenotypic methods.Abstract:
sitivityofgenome-basedresistancepredictionacrossallantibioticsforbothspecieswas0.96(95%CI:0.94‐0.98)and the specificity was 0.97 (95% CI: 0.95‐0.98). Very major and major error rates were 1.2% and 2.1%, respectively. Conclusions: Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.read more
Citations
More filters
Journal ArticleDOI
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye,Harriet Dashnow,Harriet Dashnow,Lesley Raven,Mark B. Schultz,Bernard J. Pope,Bernard J. Pope,Takehiro Tomita,Justin Zobel,Kathryn E. Holt +9 more
TL;DR: This work presents SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data, which is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment.
Journal ArticleDOI
ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Xavier Didelot,Daniel J. Wilson +1 more
TL;DR: This work uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction and finds evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582.
Journal ArticleDOI
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.
Ea Zankari,Rosa Lundbye Allesøe,Katrine Grimstrup Joensen,Lina Cavaco,Ole Lund,Frank Møller Aarestrup +5 more
TL;DR: PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
Journal ArticleDOI
Within-host evolution of bacterial pathogens
Xavier Didelot,A. Sarah Walker,Tim E. A. Peto,Derrick W. Crook,Derrick W. Crook,Daniel J. Wilson,Daniel J. Wilson +6 more
TL;DR: How whole-genome sequencing studies have advanced understanding of the mechanisms and principles of within-host genome evolution is described, and the consequences of findings such as a potent adaptive potential for pathogenicity are considered.
Journal ArticleDOI
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
TL;DR: 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.
References
More filters
Performance standards for antimicrobial susceptibility testing
TL;DR: The supplemental information presented in this document is intended for use with the antimicrobial susceptibility testing procedures published in the following Clinical and Laboratory Standards Institute (CLSI)–approved standards.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
TL;DR: SeaView version 4 combines all the functions of the widely used programs SeaView and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.
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.