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Members of the  Mycobacterium chelonae - abscessus  complex (MCAC) are close to the mycobacterial ancestor and includes both human, animal and fish pathogens. We present the genomes of 14 members of this complex: the complete genomes of  Mycobacterium salmoniphilum  and  Mycobacterium chelonae  type strains, seven  M. salmoniphilum  isolates, and five  M. salmoniphilum -like strains including strains isolated during an outbreak in an animal facility at Uppsala University. Average nucleotide identity (ANI) analysis and core gene phylogeny revealed that the  M. salmoniphilum -like strains are variants of the human pathogen  Mycobacterium franklinii  and phylogenetically close to  Mycobacterium abscessus . Our data further suggested that  M. salmoniphilum  separates into three branches named group I, II and III with the  M. salmoniphilum  type strain belonging to group II. Among predicted virulence factors, the presence of phospholipase C ( plcC ), which is a major virulence factor that makes  M. abscessus  highly cytotoxic to mouse macrophages, and that  M. franklinii  originally was isolated from infected humans make it plausible that the outbreak in the animal facility was caused by a  M. salmoniphilum -like strain. Interestingly,  M. salmoniphilum -like was isolated from tap water suggesting that it can be present in the environment. Moreover, we predicted the presence of mutational hotspots in the  M. salmoniphilum  isolates and 26% of these hotspots overlap with genes categorized as having roles in virulence, disease and defense. We also provide data about key genes involved in transcription and translation such as sigma factor, ribosomal protein and tRNA genes.

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Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains