Genome-scale analysis of Mycobacteroides abscessus clinical isolates from a university hospital

Abstract

Mycobacteroides abscessus is a rapidly growing nontuberculous mycobacterium associated with difficult-to-treat infections because of its intrinsic antimicrobial resistance and genomic adaptability. However, subspecies diversity and accessory genome dynamics remain insufficiently characterized in Thailand. Whole-genome sequencing (WGS) was performed on 105 M. abscessus clinical isolates collected at a university hospital in northeastern Thailand. Species and subspecies classifications were confirmed using genomic approaches. Genomic relatedness was assessed using average nucleotide identity (ANI), core-genome phylogeny, and single-nucleotide polymorphism (SNP)-based analyses. Antimicrobial resistance- and virulence-associated genes were identified against multiple curated databases. Pangenome structure and functional interaction patterns were evaluated through pangenome, network, and enrichment analyses. Concordant ANI, core-genome, and SNP-based analyses resolved three subspecies: subsp. abscessus (50.48%), subsp. massiliense (48.57%), and subsp. bolletii (0.95%). Phylogenetic analyses revealed genetically distinct but closely related hospital-associated clusters, suggesting local circulation patterns. Multilocus sequence typing identified predominant ST39 (29.73%), ST37 (24.32%), and ST33 (13.51%), whereas numerous unassigned STs suggested substantial unexplored genomic diversity. Genome screening revealed conserved resistance-associated genes, including erm (41), RbpA , and rpoB2 . Virulence-associated genes, including phoP , relA , icl , mbtH , and ahpC , were conserved across all isolates, supporting roles in intracellular persistence, iron acquisition, and oxidative stress defense. Pangenome analysis identified 15,230 gene clusters, comprising 3,702 core genes, 217 soft-core genes, 1,394 accessory genes, and 9,917 unique genes, indicating an open pangenome structure and substantial accessory genome diversity. Network and functional enrichment analyses demonstrated strong enrichment of translation- and ribosome-associated pathways, suggesting that translational machinery may play an important role in bacterial adaptation and cellular fitness. These observations generate hypotheses regarding the potential contribution of ribosomal protein diversity to translation efficiency under stress conditions. Overall, M. abscessus clinical isolates from northeastern Thailand comprised three genetically distinct subspecies, with subsp. abscessus and subsp. massiliense predominating. Conserved resistance- and virulence-associated genes together with an open pangenome highlight the adaptive genomic capacity of this pathogen. These findings provide a regional genomic framework to support future surveillance, infection prevention, and therapeutic strategy development.