Next-Generation Ion Torrent Sequencing of Drug Resistance Mutations in Mycobacterium tuberculosis Strains
- 1 December 2012
- journal article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 50 (12), 3831-3837
- https://doi.org/10.1128/jcm.01893-12
Abstract
A novel protocol for full-length Mycobacterium tuberculosis gene analysis of first- and second-line drug resistance was developed using the Ion Torrent Personal Genome Machine (PGM). Five genes— rpoB (rifampin), katG (isoniazid), pncA (pyrazinamide), gyrA (ofloxacin/fluoroquinolone), and rrs (aminoglycosides)—were amplified and sequenced, and results were compared to those obtained by genotypic Hain line probe assay (LPA) and phenotypic Bactec MGIT 960 analysis using 26 geographically diverse South African clinical isolates collected between July and November 2011. Ion Torrent sequencing exhibited 100% (26/26) concordance to phenotypic resistance obtained by MGIT 960 culture and genotypic rpoB and katG results by LPA. In several rifampin-resistant isolates, Ion Torrent sequencing revealed uncommon substitutions (H526R and D516G) that did not have a defined mutation by LPA. Importantly, previously uncharacterized mutations in rpoB (V194I), rrs (G878A), and pncA (Q122Stop) genes were observed. Ion Torrent sequencing may facilitate tracking and monitoring geographically diverse multidrug-resistant and extensively drug-resistant strains and could potentially be integrated into selected regional and reference settings throughout Africa, India, and China.Keywords
This publication has 21 references indexed in Scilit:
- The Beginning of therpoBGene in Addition to the Rifampin Resistance Determination Region Might Be Needed for Identifying Rifampin/Rifabutin Cross-Resistance in Multidrug-Resistant Mycobacterium tuberculosis Isolates from Southern ChinaJournal of Clinical Microbiology, 2012
- Association of mutation patterns in gyrA/B genes and ofloxacin resistance levels in Mycobacterium tuberculosisisolates from East China in 2009BMC Infectious Diseases, 2011
- Genome Analysis of Multi- and Extensively-Drug-Resistant Tuberculosis from KwaZulu-Natal, South AfricaPLOS ONE, 2009
- Pyrazinamide Resistance among South African Multidrug-Resistant Mycobacterium tuberculosis IsolatesJournal of Clinical Microbiology, 2008
- Global Incidence of Multidrug‐Resistant TuberculosisThe Journal of Infectious Diseases, 2006
- Use of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in Mycobacterium tuberculosis Complex IsolatesJournal of Clinical Microbiology, 2005
- Detection of rpoB Mutations Associated with Rifampin Resistance in Mycobacterium tuberculosis Using Denaturing Gradient Gel ElectrophoresisAntimicrobial Agents and Chemotherapy, 2005
- Susceptibility Testing with the Manual Mycobacteria Growth Indicator Tube (MGIT) and the MGIT 960 System Provides Rapid and Reliable Verification of Multidrug-Resistant TuberculosisJournal of Clinical Microbiology, 2003
- Testing of Susceptibility of Mycobacterium tuberculosis to Pyrazinamide with the Nonradiometric BACTEC MGIT 960 SystemJournal of Clinical Microbiology, 2002
- Site‐directed mutagenesis of the katG gene of Mycobacterium tuberculosis: effects on catalase–peroxidase activities and isoniazid resistanceMolecular Microbiology, 1996