ARS | Publication request: Resolution of M. bovis phylogeny using genome-wide single nucleotide polymorphisms

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 1, 2011
Publication Date: May 23, 2011
Citation: Joshi, D., Waters, W.R., Harris, B., Thacker, T.C., Palmer, M.V., Mathema, B., Krieswirth, B., Sreevatsan, S. 2011. Resolution of M. bovis phylogeny using genome-wide single nucleotide polymorphisms [abstract]. American Society for Microbiology. Abstract No. 1496.

Technical Abstract: Piecemeal analysis of Mycobacterium bovis (MBO) genomes and conventional genotyping methods have not lent to a comprehensive resolution of its genetic diversity to explain the wide range of disease phenotypes caused by this zoonotic pathogen. Conventional genotyping methods like spoligotyping and VNTR analysis that target a small hypervariable region on the genome of MBO provide anonymous biallelic information insufficient to develop MBO phylogeny. Genome-wide single nucleotide polymorphisms (SNPs) studies in M. tuberculosis have shown resolution sufficient to develop trait-allele interactions. Using the high throughput iPLEX(TM) Massarray (Sequenom), we interrogated the MBO genome for 350 loci including geneic (n =44) and intergeneic (n =306) regions for SNPs. The 350 loci studied were discovered by comparative genomics of the sequenced Mycobacterium bovis strain AF2122/97 and the BCG-Pasteur vaccine strain. A collection of 67 MBO isolates associated with bovine tuberculosis outbreaks in USA between 1990-2009 and isolated from a variety of mammalian hosts – cattle (n =26), deer (n =7), elk (n =13), elephant (n =4), swine (n =8), and humans (n =9) were used for the study. Sixty M. tuberculosis (sensu stricto) isolates from human, primate, birds, and elephants were also included in the analysis as well. Based on 206 variant SNPs between the MBO strains, five major clusters consistent with epidemiologic and other strain-typing information were identified. All the MTB s.s isolates were identical at the 350 loci examined. SNP-based phylogenetic tree provided evidence that there were multiple events of introduction of MBO into USA herds from Mexico, which over time have localized and evolved independently within the cattle and deer population of USA. The evolution of MBO also appears to be host-driven. This SNP based phylogeny provides new insights into the evolution of Mycobacterium bovis and a gateway for studying strain genotype-disease phenotype correlations which are currently underway.