Differentiating Host-Associated Variants ofMycobacterium aviumby PCR for Detection of Large Sequence Polymorphisms

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Abstract
TheMycobacterium aviumspecies consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-typeM. aviumisolates and from cattle types and sheep types ofM. aviumsubsp.paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly typeM. aviumisolates into these subgroups.