Drug Resistance Profiling and Associated Gene Mutations in <i>Mycobacterium Kansasii</i> Isolates from Turkey Using Sanger and Nanopore Sequencing

Abstract

Background: Nontuberculous mycobacteria (NTM), commonly present in the environment, are categorized into slow-growing and rapid-growing species. Mycobacterium kansasii is classified as a slow-growing mycobacterium and can cause infections in the skin and lymph nodes, similar to tuberculosis; however, pulmonary infections remain the primary cause of diseases associated with M. kansasii. Based on our literature review, this may be the first study on the distribution and drug resistance of M. kansasii isolates from varied regions of Turkey. Objectives: We determined the minimum inhibitory concentration (MIC) values of 40 M. kansasii isolates and investigated the genes that could be responsible for drug resistance in M. kansasii isolates from Turkey. Methods: A total of 40 M. kansasii isolates were collected from respiratory tract samples [sputum, bronchoalveolar lavage (BAL), and bronchial aspirates] between 2021 and 2023 at the Tuberculosis Reference Laboratory in Ankara, Turkey. Bacterial identification was confirmed by routine culture on Lowenstein-Jensen (LJ) medium followed by molecular methods. Drug susceptibility testing (DST) was performed, and genes associated with resistance (gyrA, gyrB, rpoB, rbpA, rrl) were sequenced using both Sanger and Oxford Nanopore Technologies platforms. Results: Forty isolates of M. kansasii were susceptible to amikacin (AMK), clarithromycin (CLA), linezolid (LZD), moxifloxacin (MXF), and rifabutin (RFB). Ninety percent of these isolates were resistant to ciprofloxacin (CIP) and rifampin (RIF). All isolates exhibited resistance to ethambutol (EMB), and 70% of isolates were resistant to trimethoprim/sulfamethoxazole (TMP-SMZ). We detected no mutation in the gyrA, gyrB, rbpA, and rrl genes. However, new mutations in the rpoB gene were detected in this study. Conclusions: This study highlights the need for monitoring drug susceptibility in M. kansasii isolates and the utilization of whole genome sequencing (WGS) to identify mutations and other mechanisms associated with drug resistance.