Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples.

Autor:	Brown AC; Oxford Gene Technology, Oxford, United Kingdom., Bryant JM; UCL, Division of Infection and Immunity, London, United Kingdom j.bryant@ucl.ac.uk., Einer-Jensen K; Qiagen-AAR, Aarhus, Denmark., Holdstock J; Oxford Gene Technology, Oxford, United Kingdom., Houniet DT; Oxford Gene Technology, Oxford, United Kingdom., Chan JZ; Oxford Gene Technology, Oxford, United Kingdom., Depledge DP; UCL, Division of Infection and Immunity, London, United Kingdom., Nikolayevskyy V; National Mycobacterium Reference Laboratory (NMRL), ICMS, London, United Kingdom., Broda A; National Mycobacterium Reference Laboratory (NMRL), ICMS, London, United Kingdom., Stone MJ; Dept. Microbiology, Frimley Health NHS Foundation Trust, Wexham Park Hospital, Berkshire, United Kingdom., Christiansen MT; UCL, Division of Infection and Immunity, London, United Kingdom., Williams R; UCL, Division of Infection and Immunity, London, United Kingdom., McAndrew MB; Oxford Gene Technology, Oxford, United Kingdom., Tutill H; UCL, Division of Infection and Immunity, London, United Kingdom., Brown J; UCL, Division of Infection and Immunity, London, United Kingdom., Melzer M; Barts Health NHS Trust, West Smithfield, London, United Kingdom., Rosmarin C; Barts Health NHS Trust, West Smithfield, London, United Kingdom., McHugh TD; Centre for Clinical Microbiology, UCL, Royal Free Campus, London, United Kingdom., Shorten RJ; Centre for Clinical Microbiology, UCL, Royal Free Campus, London, United Kingdom Specialist Microbiology Network, Public Health Laboratory Manchester, Manchester Royal Infirmary, Manchester, United Kingdom., Drobniewski F; National Mycobacterium Reference Laboratory (NMRL), ICMS, London, United Kingdom., Speight G; Oxford Gene Technology, Oxford, United Kingdom., Breuer J; UCL, Division of Infection and Immunity, London, United Kingdom.
Jazyk:	angličtina
Zdroj:	Journal of clinical microbiology [J Clin Microbiol] 2015 Jul; Vol. 53 (7), pp. 2230-7. Date of Electronic Publication: 2015 May 13.
DOI:	10.1128/JCM.00486-15
Abstrakt:	The rapid identification of antimicrobial resistance is essential for effective treatment of highly resistant Mycobacterium tuberculosis. Whole-genome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike for conventional molecular tests, this has previously been achievable only from cultures of M. tuberculosis. Here we describe a method utilizing biotinylated RNA baits designed specifically for M. tuberculosis DNA to capture full M. tuberculosis genomes directly from infected sputum samples, allowing whole-genome sequencing without the requirement of culture. This was carried out on 24 smear-positive sputum samples, collected from the United Kingdom and Lithuania where a matched culture sample was available, and 2 samples that had failed to grow in culture. M. tuberculosis sequencing data were obtained directly from all 24 smear-positive culture-positive sputa, of which 20 were of high quality (>20× depth and >90% of the genome covered). Results were compared with those of conventional molecular and culture-based methods, and high levels of concordance between phenotypical resistance and predicted resistance based on genotype were observed. High-quality sequence data were obtained from one smear-positive culture-negative case. This study demonstrated for the first time the successful and accurate sequencing of M. tuberculosis genomes directly from uncultured sputa. Identification of known resistance mutations within a week of sample receipt offers the prospect for personalized rather than empirical treatment of drug-resistant tuberculosis, including the use of antimicrobial-sparing regimens, leading to improved outcomes. (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)
Databáze:	MEDLINE
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