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PMID: 19047395 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis.

Applied and environmental microbiology ·Vol. 75 ·No. 3 ·2009-02-00 ·Pages 676-86

Castellanos E, Aranaz A, Gould KA, Linedale R, Stevenson K, Alvarez J, Dominguez L, de Juan L, Hinds J, Bull TJ

Abstract

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.

MeSH Terms
Animals Base Composition DNA, Bacterial/genetics Gene Duplication Gene Order Genome, Bacterial Genomic Islands Genotype Humans INDEL Mutation Microarray Analysis Mycobacterium avium subsp. paratuberculosis/classification,genetics Oligonucleotide Array Sequence Analysis Polymerase Chain Reaction/methods Polymorphism, Genetic Synteny
Chemicals
DNA, Bacterial
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Castellanos Elena
Centro de Vigilancia Sanitaria Veterinaria, Departamento Sanidad Animal, Universidad Complutense, Madrid, Spain.
Aranaz Alicia
Gould Katherine A
Linedale Richard
Stevenson Karen
Alvarez Julio
Dominguez Lucas
de Juan Lucia
Hinds Jason
Bull Tim J
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
1098-5336
DOI
10.1128/AEM.01683-08
Published
2009-02-00
Epub
2008-00-01
Pages
676-86
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC2632155
Subset
IM
Grants
Wellcome Trust · 86547 · United Kingdom
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1128/AEM.01683-08 PMC Full Text View journal details
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