Molecular Detection of Mutations Associated with First- and Second-Line Drug Resistance Compared with Conventional Drug Susceptibility Testing of Mycobacterium tuberculosis

<jats:title>ABSTRACT</jats:title> <jats:p> The emergence of multi- and extensively drug-resistant tuberculosis is a significant impediment to the control of this disease because treatment becomes more complex and costly. Reliable and timely drug susceptibility testing is critical to ensure that patients receive effective treatment and become noninfectious. Molecular methods can provide accurate and rapid drug susceptibility results. We used DNA sequencing to detect resistance to the first-line antituberculosis drugs isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB) and the second-line drugs amikacin (AMK), capreomycin (CAP), kanamycin (KAN), ciprofloxacin (CIP), and ofloxacin (OFX). Nine loci were sequenced: <jats:italic>rpoB</jats:italic> (for resistance to RIF), <jats:italic>katG</jats:italic> and <jats:italic>inhA</jats:italic> (INH), <jats:italic>pncA</jats:italic> (PZA), <jats:italic>embB</jats:italic> (EMB), <jats:italic>gyrA</jats:italic> (CIP and OFX), and <jats:italic>rrs</jats:italic> , <jats:italic>eis</jats:italic> , and <jats:italic>tlyA</jats:italic> (KAN, AMK, and CAP). A total of 314 clinical <jats:named-content xmlns:xlink="http://www.w3.org/1999/xlink" content-type="genus-species" xlink:type="simple">Mycobacterium tuberculosis</jats:named-content> complex isolates representing a variety of antibiotic resistance patterns, genotypes, and geographical origins were analyzed. The molecular data were compared to the phenotypic data and the accuracy values were calculated. Sensitivity and specificity values for the first-line drug loci were 97.1% and 93.6% for <jats:italic>rpoB</jats:italic> , 85.4% and 100% for <jats:italic>katG</jats:italic> , 16.5% and 100% for <jats:italic>inhA</jats:italic> , 90.6% and 100% for <jats:italic>katG</jats:italic> and <jats:italic>inhA</jats:italic> together, 84.6% and 85.8% for <jats:italic>pncA</jats:italic> , and 78.6% and 93.1% for <jats:italic>embB</jats:italic> . The values for the second-line drugs were also calculated. The size and scope of this study, in numbers of loci and isolates examined, and the phenotypic diversity of those isolates support the use of DNA sequencing to detect drug resistance in the <jats:named-content xmlns:xlink="http://www.w3.org/1999/xlink" content-type="genus-species" xlink:type="simple">M. tuberculosis</jats:named-content> complex. Further, the results can be used to design diagnostic tests utilizing other mutation detection technologies. </jats:p>