Independent Pyrazinamide–Bedaquiline Resistance in Mycobacterium tuberculosis Complex: A Molecular Study

Background: To determine the molecular relationship between pyrazinamide (PZA) and bedaquiline (BDQ) resistance mechanisms in multidrug-resistant tuberculosis (MDR-TB) and drug-susceptible Mycobacterium tuberculosis (M. tuberculosis) isolates to improve treatment strategies. Methods: Phenotypic drug susceptibility testing (DST), resistance gene amplification and sequencing (pncA, panD, hadC, and Rv0678), and efflux pump gene expression (mmpS5 and mmpL5) by qRT-PCR were performed on 71 clinical MTBC isolates from seven provinces in Southern Türkiye (2022-2023). Results: PZA resistance was closely associated with MDR-TB (χ² = 38.0, p < 0.0001), exclusively detected in MDR isolates (42% overall; 73% of MDR). pncA mutations were detected in 77% of PZA-resistant isolates with strong genotype-phenotype correlation (p = 0.009, r = 0.45), while panD mutations were present in 40% and showed less association (p = 0.14). No hadC or Rv0678 mutations were identified despite significant overexpression of efflux genes mmpS5 and mmpL5 in MDR strains (p < 0.001). Conclusions: PZA and BDQ resistance arise through distinct, non-overlapping mechanisms. PZA-resistant MDR-TB without Rv0678 mutations confirms bedaquiline's independent therapeutic value and success in treating PZA-resistant cases.