| Mycobacterium avium subspecies paratuberculosis (Map) is the causative agent of Johne's disease (JD) in cattle and other ruminants, which has a considerable impact on dairy health and production, and is also concerned for a hypothetical association between Map and Crohn's disease in humans. To test the hypothesis that Map strains from different host species or geographic origins are genetically distinguishable from each other, the genome sequence of a common cattle isolate, Map K-10 was characterized, and several strain differentiation methods based on the availability of the complete genome sequence of Map were evaluated.; The completion of Map K-10 genome sequence allowed for identifying all potential genes including unique genes, understanding of physiology and pathogenesis process including mycobactin synthesis, virulence factors, and evolutionary relationship. Multi-locus short sequence repeats (MLSSRs) were identified and used as markers for Map strain differentiation. MLSSR and pulse field gel electrophoresis (PFGE) patterns were compared in 268 isolates and results show that these two methods have good concordance and MLSSR has higher discriminatory power. The utility of variable-number tandem repeats (VNTRs) was tested in 36 Map isolates and results suggest that Map isolates can be grouped into 3 distinct clusters as sheep, cattle, and bison cluster, providing genetic evidence for bison type strains as a distinctive subset of Map. Both MLSSR and VNTR based analyses are rapid, sensitive, and reliable methods and can be used for strain differentiation of Map as first-line tools.; Results of single nucleotide polymorphisms (SNPs) at 95 loci in 15 Map isolates confirmed that isolates recovered from sheep are a distinct group and also identified specific SNP patterns in isolates recovered from bison. A whole genome analysis of a Map K-10 and an isolate recovered from a Crohn's disease patient confirmed restricted allelic variation in Map and clearly showed the considerable similarity in sequence identity between Map isolates recovered from cattle or from humans. Based on synonymous SNP analysis, divergence of Map and M. avium subsp. avium is estimated ∼4 million years ago and Map has likely become widespread in distribution with domestication of cattle. |
