Rationally tailored antibiotic selection circumvents toxin-mediated evasion of killing in Mycobacterium abscessus

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Abstract
Among clinically important non-tuberculous mycobacteria, Mycobacterium abscessus (Mab) has a large and highly dynamic accessory genome within an open pangenome, contributing traits that enhance drug resistance, bacterial persistence, stress survival, metabolic flexibility, and/or virulence. Defining how accessory loci promote survival during antimicrobial exposure is essential for understanding why Mab frequently evades killing by standard drug regimens and for improving therapeutic outcomes. We recently identified a potent accessory toxin–antitoxin (TA) system, VapB5-VapC5, that substantially enhances the already formidable drug resistance capacity of Mab clinical isolates. Acquisition of this single system reprograms Mab physiology to inhibit growth, activate the WhiB7 regulon, and promote ribosome accumulation. Here, we further define the contribution of the active component of this TA system, the VapC5 toxin, by assessing its impact on a more comprehensively defined WhiB7 regulon. We also studied the effects of VapC5 on growth, persistence, and the Mab transcriptome independently of WhiB7. Finally, we determined that VapC5-mediated resistance is mechanism-dependent. Because our previous study showed that VapC5 promotes survival during exposure to frontline antimicrobials that target cell-wall biosynthesis or protein translation, we reasoned that antibiotics with distinctly different mechanisms of action would be more likely to retain activity. As predicted, DNA gyrase or RNA polymerase inhibitors circumvented VapC5-mediated resistance and retained in vitro efficacy. These findings establish VapC5 as a broad physiological modulator that selectively reshapes Mab antimicrobial susceptibility based on drug mechanism. Screening Mab clinical isolates for acquisition of this accessory VapBC5 toxin-antitoxin system could risk-stratify treatment decisions by directing clinicians toward existing antibiotics targeting processes unaffected by VapC5, thereby improving treatment outcomes.

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