Journal
MICROBIAL GENOMICS
Volume 3, Issue 10, Pages -Publisher
MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000131
Keywords
antimicrobial resistance; whole genome sequencing; genotyping; bacteria; sequence typing
Categories
Funding
- Wellcome Trust [206194]
- Biotechnology and Biological Sciences Research Council [BB/M014088/1]
- BBSRC [BB/M014088/1] Funding Source: UKRI
- MRC [MR/L015080/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/M014088/1] Funding Source: researchfish
- Medical Research Council [MR/L015080/1] Funding Source: researchfish
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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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