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Mycobacterium chelonae  is a member of the  Mycobacterium chelonae-abscessus  complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previously identified rapidly-growing, non-tuberculous  Mycobacterium  sp. isolates cultured from biofilms, fish, reptiles, mammals, including humans, and three ATCC reference strains were evaluated with nine  M .  chelonae-abscessus  complex whole genome sequences from GenBank by phylogenomic analysis, targeted gene comparisons, and  in-vitro  antimicrobial susceptibility patterns to assess strain variation among isolates from different sources. Results revealed minimal genetic variation among the  M .  chelonae  strains. However, the core genomic alignment and SNP pattern of the complete 16S rRNA sequence clearly separated the turtle type strain ATCC 35752 T  from the clinical isolates and human reference strain “ M .  chelonae  chemovar  niacinogenes ” ATCC 19237, providing evidence of two distinct subspecies. Concatenation of the partial  rpoB  (752 bp) and complete  hsp65  (1,626 bp) sequence produced the same species/subspecies delineations as the core phylogeny. Partial  rpoB  and  hsp65  sequences identified all the clinical isolates to the appropriate species level when respective cut-offs of 98% and 98.4% identity to the  M .  chelonae  type strain ATCC 35752 T  were employed. The human strain, ATCC19237, was the most representative strain for the evaluated human, veterinary, and environmental strains. Additionally, two isolates were identified as  Mycobacterium saopaulense , its first identification in a non-fish or non-human host.

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Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns