# ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Article · Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR

- Archive id: doi:10.1099/mgen.0.000131
- Published: 2017-09-04
- Venue: Microbial genomics
- DOI: https://doi.org/10.1099/mgen.0.000131
- PMID: 29177089
- PMCID: PMC5695208
- Citations: 530
- Source URL: https://doi.org/10.1099/mgen.0.000131
- PDF: https://europepmc.org/articles/PMC5695208/pdf
- Provenance: europepmc

## 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.

_Abstract reproduced under CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)._

Topics: [Infectious Disease, Vaccines & Antimicrobial Resistance](https://space-kitty.com/topics/infectious-disease-amr)

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