title: Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis.
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.
authors.affiliation: Centro de Vigilancia Sanitaria Veterinaria, Departamento Sanidad Animal, Universidad Complutense, Madrid, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Castellanos
authors.forename: Alicia
authors.initials: A
authors.lastname: Aranaz
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Gould
authors.forename: Richard
authors.initials: R
authors.lastname: Linedale
authors.forename: Karen
authors.initials: K
authors.lastname: Stevenson
authors.forename: Julio
authors.initials: J
authors.lastname: Alvarez
authors.forename: Lucas
authors.initials: L
authors.lastname: Dominguez
authors.forename: Lucia
authors.initials: L
authors.lastname: de Juan
authors.forename: Jason
authors.initials: J
authors.lastname: Hinds
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Bull
mesh_terms: D000818:Animals; D001482:Base Composition; D004269:DNA, Bacterial / Q000235:genetics*; D020440:Gene Duplication; D023061:Gene Order; D016680:Genome, Bacterial; D044404:Genomic Islands; D005838:Genotype; D006801:Humans; D054643:INDEL Mutation; D046228:Microarray Analysis; D016927:Mycobacterium avium subsp. paratuberculosis / Q000145:classification* / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D026801:Synteny
chemical_list: D004269:DNA, Bacterial