Genomic comparison of clinical strains of Mycobacterium shinjukuense in Japan reveals low diversity and stable genome structures.

Mycobacterium shinjukuense, a rare non-tuberculous mycobacterial species closely related to Mycobacterium tuberculosis, remains poorly characterized at the genomic level. To obtain insights into its intraspecies genomic diversity and structure variation, we performed whole-genome sequencing on 18 clinical strains of M. shinjukuense collected from Japan between 2010 and 2017. Phylogenetic analysis revealed limited overall genetic diversity, with several clonal clusters likely representing identical strains. The phylogeny exhibited a largely star-like topology with few single nucleotide variations accumulated over time, suggesting a clonal expansion. Complete genome sequencing of five representative strains revealed high synteny, with no large-scale rearrangements, suggesting stable genomic structures. One strain, MSJ-01, harboured a unique 30 kb insertion region, possibly acquired via horizontal gene transfer. These findings provide insights into the genomic diversity and structure of M. shinjukuense, suggesting both its evolutionary stability and its potential to incorporate foreign DNA. This work expands upon available genomic resources and supports the utility of M. shinjukuense as a model for understanding genome evolution in the M. tuberculosis-associated phylotype lineage.