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Differentiating Host-Associated Variants of Mycobacterium avium by PCR for Detection of Large Sequence Polymorphisms

McGill University Health Centre, Montreal, Quebec, Canada,¹ National Institute of Public Health and the Environment, 3720BA Bilthoven, The Netherlands,² AgResearch, Wallaceville Animal Research Centre, Upper Hutt, New Zealand³

Received 13 October 2005/ Returned for modification 8 December 2005/ Accepted 28 December 2005

The Mycobacterium avium species 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-type M. avium isolates and from cattle types and sheep types of M. avium subsp. 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 type M. avium isolates into these subgroups.

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