Activity of omadacycline and comparator agents against rapidly growing mycobacteria by broth microdilution and whole genome sequencing

ABSTRACT Pulmonary infections caused by rapidly growing mycobacteria (RGM), such as Mycobacteroides abscessus , are challenging to treat, highlighting the need for new therapeutic options. This study evaluated the in vitro activity of omadacycline against RGM and investigated the influence of tetracycline resistance mechanisms on its in vitro activity. In vitro susceptibility to omadacycline and comparator antimicrobials was assessed by broth microdilution against 476 geographically diverse RGM isolates from the United States. Omadacycline minimal inhibitory concentration (MIC) distributions were compared between cystic fibrosis (CF) and non-CF RGM isolates. Variation in the TetR–TetX operon and the rrl , rrs , and erm (41) genes was evaluated by whole genome sequencing. Omadacycline exhibited low MIC values across all RGM species (MIC 50 /MIC 90 : 0.25/0.5 µg/mL). CF isolates showed a modest shift toward higher omadacycline MIC values ( P = 0.001). The activity of comparator antimicrobials varied by species, whereas omadacycline was consistent and comparable to tigecycline. The TetR–TetX operon was present in all sequenced isolates, with variable amino acid sequences across species. These variations did not significantly affect omadacycline or tigecycline activity, whereas doxycycline and minocycline remained largely inactive regardless of TetR–TetX variation. The rrs A1408G mutation was identified in 6% of M. abscessus isolates, and rrl mutations were identified in 4% of isolates. The T28C erm (41) sequevar was present in 80% of M. abscessus subsp. abscessus and 100% of M. abscessus subsp. bolletii , whereas 100% of M. abscessus subsp. massiliense exhibited a truncated erm (41). Omadacycline consistently demonstrated potent in vitro activity across RGM species regardless of TetR–TetX operon variation, supporting its potential role in treating RGM infections. IMPORTANCE Rapidly growing mycobacteria (RGM) are a group of bacteria that often resist common antibiotics, making the infections they cause hard to treat. In this study, we tested omadacycline, a newer antibiotic in the tetracycline class, against a large collection of these bacteria collected from patients across the United States. We found that omadacycline showed consistent activity against different RGM species, requiring low concentrations to inhibit bacterial growth in laboratory testing. These findings support further evaluation of omadacycline as a potential treatment option for patients with RGM infections, which can be challenging to manage.