Abstract
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.
Highlights
Www.nature.com/scientificreports seems to be the most important species infecting a wide array of different fish, in particular in warm water systems, while the coldwater pathogen Mche infects predominantly salmonid species[2]
As exemplified by the emerging pathogen Mycobacterium abscessus (Mabs), members of the Mycobacterium chelonae-abscessus complex (MCAC)-complex display resistance to many clinically relevant antibiotics and infections caused by these mycobacteria can be problematic and treatment requires the use of other antibiotics than in treatment of tuberculosis[11]
Whole genome average nucleotide identity and core gene phylogeny further suggested that the Mycobacterium salmoniphilum (Msal)-like isolates should be referred to as Mycobacterium franklinii (Mfra) strains and that they are phylogenetically close to Mabs
Summary
Www.nature.com/scientificreports seems to be the most important species infecting a wide array of different fish, in particular in warm water systems, while the coldwater pathogen Mche infects predominantly salmonid species[2]. As exemplified by the emerging pathogen Mabs, members of the MCAC-complex display resistance to many clinically relevant antibiotics and infections caused by these mycobacteria can be problematic and treatment requires the use of other antibiotics than in treatment of tuberculosis[11]. Together this imposes a potential risk for selecting antibiotic resistant microbes and thereby constitutes a threat to animal and human health[9,13,14,15,16]. Our data further suggest that Msal constitute three separate groups
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