ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Martin Hunt; Alison E. Mather; Leonor Sánchez-Busó; Andrew J. Page; Julian Parkhill; Jacqueline A. Keane; Simon R. Harris

doi:10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Martin Hunt
, Alison E. Mather
, Leonor Sánchez-Busó
, Andrew J. Page
, Julian Parkhill
, Jacqueline A. Keane
, Simon R. Harris

Research output: Contribution to journal › Article › peer-review

540 Citations (Scopus)

8 Downloads (Pure)

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.

Original language	English
Article number	000131
Journal	Microbial Genomics
Volume	3
Issue number	10
Early online date	4 Sept 2017
DOIs	https://doi.org/10.1099/mgen.0.000131
Publication status	Published - 1 Oct 2017
Externally published	Yes

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1099/mgen.0.000131Licence: CC BY

Published_VersionFinal published version, 510 KBLicence: CC BY

Alison Mather
- A.Matheruea.acuk
- Faculty of Medicine and Health Sciences - ISP Leader
- Norwich Medical School - Honorary Professor
- Metabolic Health - Member
Person: Honorary, Research Group Member, Academic, Teaching and Research

Cite this

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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.",

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AU - Sánchez-Busó, Leonor

AU - Page, Andrew J.

AU - Parkhill, Julian

AU - Keane, Jacqueline A.

AU - Harris, Simon R.

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AB - 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.

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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Abstract

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Alison Mather

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