Investigation of delamanid, bedaquiline, and linezolid resistance rates and related gene mutations in multidrug-resistant Mycobacterium tuberculosis in regional tuberculosis reference laboratories of Iran

So far, there are scarce data on resistance to delamanid (DLM), bedaquiline (BDQ), and linezolid (LZD) antibiotics and related gene mutations in multidrug-resistant Mycobacterium tuberculosis (MDR M. tuberculosis) from Iran. Hence, this study aimed to investigate the DLM, BDQ, and LZD resistance rates and related gene mutations in MDR M. tuberculosis in regional tuberculosis reference laboratories of Iran. In this cross-sectional study, MDR M. tuberculosis isolates (resistant to antibiotics rifampicin and isoniazid) were collected from sputum samples of tuberculosis patients referred to several regional tuberculosis reference laboratories in Iran. The resistance against DLM, BDQ, and LZD antibiotics was evaluated using the proportion method on the Middlebrook 7H11 agar culture medium. The minimum inhibitory concentration (MIC) of three antibiotics was evaluated using the broth microdilution method. Mutations in genes that contributed to resistance to antibiotics DLM (fbiA, fbiC, ddn, fgd1), BDQ (atpE, pepQ, Rv0678), and LZD (rrl and rplC) were investigated by polymerase chain reaction (PCR) and sequencing. This study examined 29 clinical MDR M. tuberculosis isolates. These isolates were collected from 68.9% (20/29) males and 31.1% (9/29) females with a mean age of 40 years (ranged 30–70 years). The resistance rate to DLM, BDQ, and LZD was 27.6% (n = 8/29), 0.0% (n = 0/29), and 6.8% (n = 2/29), respectively. The range of MIC for DLM was 0.12–0.48 µg/ml. Meanwhile, the 2 LZD-resistant isolates showed MIC of 2.0 µg/ml. All MDR M. tuberculosis isolates with phenotypic resistance to DLM (8 isolates) contained mutations in one of the fgd1, fbiA, and fbiC genes. A mutation was identified in the 1090 bp fragment of the fgd1 gene at position 839 in five isolates. Additionally, the 2386 bp fragment of the fbiC gene revealed mutations at positions 266 and 952 in three isolates. Also, two DLM-resistant isolates exhibited two mutations at position 145 and 960 in the 1136 bp fragment of fbiA. No genetic mutations were detected in ddn, atpE, pepQ, and Rv0678 genes. Two LZD-resistant isolates exhibited mutations in the rplc gene at position 460 within the 933 bp fragment, and in the rrl gene at positions 2576 and 2814 within the 1772 bp fragment. This study found multiple mutations in the fgd1, fbiA, fbiC, rplc, and rrl genes that were responsible for the development of DLM and LZD resistance in MDR M. tuberculosis isolates in Iran. More research is needed to understand the underlying mechanisms of resistance to these antibiotics.