Ancient and recent differences in the susceptibility of Mycobacterium tuberculosis complex to pretomanid

BackgroundPretomanid (Pa) is the most recently approved anti-tuberculosis drug. Its clinical use calls for a robust phenotypic antimicrobial susceptibility testing (AST) method with a properly set breakpoint.MethodsThe Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six international laboratories to determine the minimum inhibitory concentrations (MICs) of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) isolates to establish the epidemiological cut-off value (ECOFF) for Pa. MICs were correlated with whole genome sequencing data to study the genetic basis of differences in the susceptibility to Pa.ResultsWe observed ancient differences in the susceptibility to Pa among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4, and 7 of M. tuberculosis, resulting in an ECOFF of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (=8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis isolates. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by changes in the known Pa resistance genes.ConclusionsIn light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by the European Medicines Agency must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development and when defining breakpoints for AST.