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<jats:title>Abstract</jats:title> <jats:p>The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for <jats:italic>Staphylococcus aureus</jats:italic> and <jats:italic>Mycobacterium tuberculosis</jats:italic> in a software package (‘Mykrobe predictor’) that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For <jats:italic>S</jats:italic>. <jats:italic>aureus</jats:italic>, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, <jats:italic>n</jats:italic>=470). For <jats:italic>M</jats:italic>. <jats:italic>tuberculosis</jats:italic>, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, <jats:italic>n</jats:italic>=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.</jats:p>

Original publication

DOI

10.1038/ncomms10063

Type

Journal

Nature Communications

Publisher

Springer Science and Business Media LLC

Publication Date

22/12/2015

Volume

6