Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing.

Journal of Clinical Microbiology
Ronan M DoyleJudith Breuer

Abstract

The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster h...Continue Reading

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Citations

Sep 27, 2018·The New England Journal of Medicine·Helen Cox, Valerie Mizrahi
Nov 2, 2018·Journal of Clinical Microbiology·Michelle SuTimothy D Read
Sep 25, 2019·Nature Reviews. Urology·Asif MuneerAlimuddin Zumla
Dec 13, 2019·PLoS Neglected Tropical Diseases·Malgorzata A DomagalskaJean-Claude Dujardin
Oct 30, 2019·American Journal of Respiratory Cell and Molecular Biology·Sharon M CarneyStavros Garantziotis
Oct 20, 2018·PLoS Pathogens·Matthias I GröschelMatthias Merker
Jul 29, 2020·Journal of Clinical Microbiology·Sophie GeorgeKate E Dingle
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May 7, 2019·Frontiers in Microbiology·Thi Ngoc Anh NguyenThi Van Anh Nguyen
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Oct 12, 2018·Microbial Genomics·Michael A MartinWilliam P Hanage
Jun 19, 2019·Nature Reviews. Microbiology·Conor J MeehanAnnelies Van Rie
Jan 12, 2019·Tuberculosis Research and Treatment·Thato IketlengTulio de Oliveira
Jun 13, 2020·Nature Medicine·Allison BlackTrevor Bedford
Sep 29, 2020·Frontiers in Cellular and Infection Microbiology·Ya HeZhongshun Zhang
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Jan 30, 2021·Pathogens and Disease·Yoohyun HwangSungweon Ryoo
Apr 27, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Hans-Peter GrobbelStefan Niemann

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Datasets Mentioned

BETA
PRJEB21685

Methods Mentioned

BETA
PCR
DNA assay

Software Mentioned

Picard
R package seqinr
BBmap
freebayes
RAxML
ANNOVAR
Trim Galore

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