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Applied and Environmental Microbiology, February 2009, p. 676-686, Vol. 75, No. 3
0099-2240/09/$08.00+0     doi:10.1128/AEM.01683-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Discovery of Stable and Variable Differences in the Mycobacterium avium subsp. paratuberculosis Type I, II, and III Genomes by Pan-Genome Microarray Analysis{triangledown} ,{dagger}

Elena Castellanos,1 Alicia Aranaz,1 Katherine A. Gould,2 Richard Linedale,2 Karen Stevenson,3 Julio Alvarez,1 Lucas Dominguez,1 Lucia de Juan,1 Jason Hinds,2 and Tim J. Bull2*

Centro de Vigilancia Sanitaria Veterinaria, Departamento Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain,1 Division of Cellular and Molecular Medicine, St. George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom,2 Moredun Research Institute, Division of Control of Bacterial Diseases, Pentlands Science Park, Bush Loan EH26 0PZ, Penicuik, United Kingdom3

Received 21 July 2008/ Accepted 21 November 2008

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

* Corresponding author. Mailing address: Division of Cellular and Molecular Medicine, St. George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom. Phone: 44 (0)208 725 5580. Fax: 44 (0)208 725 2812. E-mail: tim.bull{at}sgul.ac.uk

{triangledown} Published ahead of print on 1 December 2008.

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

Applied and Environmental Microbiology, February 2009, p. 676-686, Vol. 75, No. 3
0099-2240/09/$08.00+0     doi:10.1128/AEM.01683-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Castellanos, E., Aranaz, A., de Juan, L., Alvarez, J., Rodriguez, S., Romero, B., Bezos, J., Stevenson, K., Mateos, A., Dominguez, L. (2009). Single Nucleotide Polymorphisms in the IS900 Sequence of Mycobacterium avium subsp. paratuberculosis Are Strain Type Specific. J. Clin. Microbiol. 47: 2260-2264 [Abstract] [Full Text]  


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