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Journal of Bacteriology, April 2005, p. 2406-2415, Vol. 187, No. 7
0021-9193/05/$08.00+0     doi:10.1128/JB.187.7.2406-2415.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Comparative Genomic Hybridizations Reveal Genetic Regions within the Mycobacterium avium Complex That Are Divergent from Mycobacterium avium subsp. paratuberculosis Isolates{dagger}

Michael L. Paustian,1* Vivek Kapur,2 and John P. Bannantine1

National Animal Disease Center, U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa,1 Biomedical Genomics Center, University of Minnesota, St. Paul, Minnesota2

Received 5 November 2004/ Accepted 22 December 2004

Mycobacterium avium subsp. paratuberculosis is genetically similar to other members of the Mycobacterium avium complex (MAC), some of which are nonpathogenic and widespread in the environment. We have utilized an M. avium subsp. paratuberculosis whole-genome microarray representing over 95% of the predicted coding sequences to examine the genetic conservation among 10 M. avium subsp. paratuberculosis isolates, two isolates each of Mycobacterium avium subsp. silvaticum and Mycobacterium avium subsp. avium, and a single isolate each of both Mycobacterium intracellulare and Mycobacterium smegmatis. Genomic DNA from each isolate was competitively hybridized with DNA from M. avium subsp. paratuberculosis K10, and open reading frames (ORFs) were classified as present, divergent, or intermediate. None of the M. avium subsp. paratuberculosis isolates had ORFs classified as divergent. The two M. avium subsp. avium isolates had 210 and 135 divergent ORFs, while the two M. avium subsp. silvaticum isolates examined had 77 and 103 divergent ORFs. Similarly, 130 divergent ORFs were identified in M. intracellulare. A set of 97 ORFs were classified as divergent or intermediate in all of the nonparatuberculosis MAC isolates tested. Many of these ORFs are clustered together on the genome in regions with relatively low average GC content compared with the entire genome and contain mobile genetic elements. One of these regions of sequence divergence contained genes homologous to a mammalian cell entry (mce) operon. Our results indicate that closely related MAC mycobacteria can be distinguished from M. avium subsp. paratuberculosis by multiple clusters of divergent ORFs.

* Corresponding author. Mailing address: National Animal Disease Center, USDA-ARS, 2300 North Dayton Ave., Ames, IA 50010. Phone: (515) 663-7979. Fax: (515) 663-7458. E-mail: mpaustia{at}nadc.ars.usda.gov.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, April 2005, p. 2406-2415, Vol. 187, No. 7
0021-9193/05/$08.00+0     doi:10.1128/JB.187.7.2406-2415.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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