Mycobacterium aviumsubsp.paratuberculosisandM. aviumsubsp.aviumAre Independently Evolved Pathogenic Clones of a Much Broader Group ofM. aviumOrganisms

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Abstract
Mycobacterium aviumcomprises organisms that share the same species designation despite considerable genomic and phenotypic variability. To determine the degree and nature of variability between subspecies and strains ofM. avium, we used multilocus sequencing analysis, studying 56 genetically diverse strains ofM. aviumthat included all described subspecies. In total, 8,064 bp of sequence from 10 gene loci were studied, with 205 (2.5%) representing variable positions. The majority (149/205) of these variations were found amongM. aviumsubsp.hominissuisorganisms. Recombination was also evident in this subspecies. In contrast, there was comparatively little variability and no evidence of recombination within the pathogenic subspecies,M. aviumsubsp.paratuberculosis,M. aviumsubsp.avium, andM. aviumsubsp.silvaticum.Phylogenetic analysis showed thatM. aviumsubsp.aviumandM. aviumsubsp.silvaticumstrains clustered together on one branch, while a distinct branch definedM. aviumsubsp.paratuberculosisorganisms. Despite the independent origin of these pathogenic subspecies, an analysis of their rates of nonsynonymous (dN) to synonymous (dS) substitutions showed increased dN/dS ratios for both: 0.67 forM. aviumsubsp.paratuberculosisand 0.50 forM. aviumsubsp.avium/M. aviumsubsp.silvaticum, while the value was 0.08 forM. aviumsubsp.hominissuisorganisms. In conclusion,M. aviumsubsp.hominissuisrepresents a diverse group of organisms from which two pathogenic clones (M. aviumsubsp.paratuberculosisandM. aviumsubsp.avium/M. aviumsubsp.silvaticum) have evolved independently.