An exploratory study on the application of nanopore sequencing for detecting Mycobacterium tuberculosis drug resistance in respiratory specimens
Abstract
BACKGROUND: This study aimed to evaluate the diagnostic efficacy of nanopore sequencing for Mycobacterium tuberculosis (MTB) drug resistance in respiratory specimens from pulmonary tuberculosis (PTB) patients. It compared it to the Xpert MTB/RIF and fluorescent polymerase chain reaction (PCR) melting curve to explore the validity and feasibility of detecting MTB drug resistance in respiratory specimens.
METHODS: This study retrospectively analyzed 52 respiratory specimens. The proportional method applied the phenotypic drug susceptibility test (pDST) to respiratory specimens. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), consistency statistic (kappa) with phenotypic drug susceptibility testing (pDST), and the area under the curve (AUC) from the receiver operating characteristic (ROC) curve were calculated for nanopore sequencing, Xpert MTB/RIF, and fluorescent PCR melting curve. These calculations used the pDST results as the reference standard.
RESULTS: Among the resistance mutation genes detected by nanopore sequencing, rpoB, and katG were the most frequent, followed by embB, rpsL, gyrA, inhA, ahpC, gyrB, gid, and rrs. In bronchoalveolar lavage fluid (BALF) specimens, nanopore sequencing showed high sensitivity (100.00%,90.32%,82.35%,82.35%,100.00%,76.92%), specificity (70.00%,81.82%,88.00%,96.00%93.75%,93.10%0.100.00%), and AUC values (0.85,0.86,0.85, 0.89,0.97,0.85) for rifampicin (RIF), isoniazid (INH), ethambutol (EMB),…
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Evidence Hub reads this as a cohort study, done in people. Its evidence level is 3 of 5 (Moderate · trial / cohort / secondary analysis). Trials without a large randomized design, cohorts and secondary analyses give moderate evidence.
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