Acquisition of a toxin-antitoxin system within a mobile genetic element likely enhances Mycobacterium abscessus fitness by enforcing cargo retention

Abstract

ABSTRACT Infections caused by the emerging pathogen Mycobacterium abscessus (Mab) require prolonged multidrug treatment regimens that frequently fail because its accessory genome has incorporated a daunting array of poorly defined resistance mechanisms. However, the processes governing acquisition and retention of new genetic material within the Mab accessory genome remain poorly understood. Here, we first identified two Mab clinical strains that harbor the same uncharacterized toxin-antitoxin (TA) system at different genomic positions. Using computational analyses of the surrounding DNA context, we discovered that each TA system resides within identical mobile genetic element (MGE) cassettes whose positions exchange between the two strains via site-specific recombinases. We then applied a specialized 5′ RNA-seq approach to identify initiator tRNAfMet as the exclusive RNA target of the VapC2 TA toxin residing within the MGE. VapC2-mediated tRNAfMet inactivation by cleavage at its anticodon stem loop leads to growth arrest and global translation inhibition. This activity ensures stable inheritance of the MGE and its resident cargo genes through a mechanism similar to postsegregational killing. Our findings uncover the mechanism for durable expansion of the Mab accessory genome and suggest a selective advantage whereby toxin-mediated entry into a reversible growth-arrested state may reduce antibiotic susceptibility. Together, these results illustrate how retention of horizontally acquired MGEs containing a potent TA system can drive adaptive genome evolution to enhance fitness in this highly drug-resistant pathogen. IMPORTANCE Mycobacterium abscessus (Mab) causes chronic lung disease and skin and soft tissue infections, posing a major threat to individuals with cystic fibrosis, underlying lung disease, lung transplants, or weakened immune systems. Unlike Mycobacterium tuberculosis, Mab has a large and highly plastic accessory genome generally thought to be predominantly shaped by horizontal gene transfer and recombination. However, the mechanisms that stabilize newly acquired genetic material in this pathogen remain poorly understood. Here, we identify a toxin-antitoxin (TA) system embedded within a mobile genetic element (MGE) predicted to enforce stable retention of the MGE through a mechanism similar to postsegregational killing. The toxin inactivates initiator tRNAfMet, inducing reversible growth arrest that likely reduces antibiotic efficacy. By functioning as an addiction module, this TA system also ensures stable inheritance of co-transferred accessory genes within the MGE, providing a mechanism for long-term retention of horizontally acquired genetic material that enhances pathogen fitness. Mycobacterium abscessus (Mab) causes chronic lung disease and skin and soft tissue infections, posing a major threat to individuals with cystic fibrosis, underlying lung disease, lung transplants, or weakened immune systems. Unlike Mycobacterium tuberculosis, Mab has a large and highly plastic accessory genome generally thought to be predominantly shaped by horizontal gene transfer and recombination. However, the mechanisms that stabilize newly acquired genetic material in this pathogen remain poorly understood. Here, we identify a toxin-antitoxin (TA) system embedded within a mobile genetic element (MGE) predicted to enforce stable retention of the MGE through a mechanism similar to postsegregational killing. The toxin inactivates initiator tRNAfMet, inducing reversible growth arrest that likely reduces antibiotic efficacy. By functioning as an addiction module, this TA system also ensures stable inheritance of co-transferred accessory genes within the MGE, providing a mechanism for long-term retention of horizontally acquired genetic material that enhances pathogen fitness.