ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Hunt, Martin
Mather, Alison E
Sánchez-Busó, Leonor
Page, Andrew J
Parkhill, Julian https://orcid.org/0000-0002-7069-5958
Abstract
Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.
Description
Keywords
antimicrobial resistance, bacteria, genotyping, sequence typing, whole genome sequencing, Animals, Drug Resistance, Microbial, Enterococcus faecium, Genomics, Humans, Infections, Neisseria gonorrhoeae, Shigella sonnei, Software
Journal Title
Microb Genom
Conference Name
Journal ISSN
2057-5858
2057-5858
2057-5858
Volume Title
3
Publisher
Microbiology Society
Publisher DOI
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/M014088/1)