ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Issue 10 (4th September 2017)

• Record Type: Journal Article
• Authors: Hunt, Martin; Mather, Alison E; Sánchez-Busó, Leonor; Page, Andrew J; Parkhill, Julian; Keane, Jacqueline A; Harris, Simon R
• Is Part Of: Microbial genomics. Volume 3:Issue 10(2017)
• Publication Date: 2017-09-04
• Subjects: antimicrobial resistance -- whole genome sequencing -- genotyping -- bacteria -- sequence typing; Microbial genomics -- Periodicals; 572.8629
• DOI: 10.1099/mgen.0.000131
• Languages: English
• ISSNs: 2057-5858

Abstract

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.