Single nucleotide polymorphisms in the Mycobacterium bovis genome resolve phylogenetic relationships.

Mycobacterium bovis isolates carry restricted allelic variation yet exhibit a range of disease phenotypes and host preferences. Conventional genotyping methods target small hypervariable regions of the M. bovis genome and provide anonymous biallelic information that is insufficient to develop phylogeny. To resolve phylogeny and establish trait-allele associations, we interrogated 75 M. bovis and 61 M. tuberculosis genomes for single nucleotide polymorphisms (SNPs), using iPLEX MassArray (Sequenom Inc., CA) technology. We indexed nucleotide variations in 306 genic and 44 intergenic loci among isolates derived from outbreaks in the United States from 1991 to 2010 and isolated from a variety of mammalian hosts. Two hundred six variant SNPs classified the 136 isolates and 4 previously sequenced strains (AF2122/97, BCG Pasteur, H37Rv, and CDC1551) into 5 major "SNP cluster groups." M. bovis isolates clustered into three major lineages based on 118 variant SNPs, while 84 SNPs differentiated the M. bovis BCG lineage from the virulent isolates. Forty-nine of the 51 human M. tuberculosis isolates were identical at all 350 loci studied. Thus, SNP-based analyses resolved the genotypic differences within M. bovis strains and differentiated these strains from M. tuberculosis strains representing diversity in time and space, providing population genetic frameworks that may aid in identifying factors responsible for the wide host range and disease phenotypes of M. bovis.