The minimum spanning tree was created based on the categorical coefficient and the priority rule ‘highest number of single-locus variants’. A detailed description of analysis using minimum spanning tree can be found

in the study by Schouls et al. [14]. Results Identification of MIRUs Four [6] and eight MIRU-VNTR [7] have been already described for M. avium and M. paratuberculosis, respectively. Because of the phylogenetic similarity between these species and M. intracellulare, it was predicted that several of these MIRU-VNTR could also be used in typing M. intracellulare isolates [15]. Thus we included these MIRU-VNTR loci, named MIRU 1 through 4 (Bull et al.), MIRU 32, 292, X3, 25, 3, 7, 10, and 47 (Thibault et al.), in Selleck BGJ398 our study. The analysis of the genome of M. avium 104 identified 120 Tandem Repeat (TR) sequences of which 16 were selected based on their degree of homology and their size (MIN 1 through MIN 16). Examination of the 353 contigs of M. intracellulare ATCC 13950 identified 310

TRs of which 17 were used in the study (MIN 17 through MIN 33). Thus a total of 45 TR loci were studied. The polymorphism of the selected 45 TR loci was initially investigated on a set of nine randomly chosen isolates of M. intracellulare (isolates 2 through 10), as well as the reference strain M. intracellulare ATCC 13950 (strain 1). Thirty-four MIRU-VNTR were absent NVP-BEZ235 solubility dmso during amplification of one or more isolates while four MIRU-VNTR did not demonstrate polymorphism on the isolates tested, they were thus eliminated. One of the 12 MIRU-VNTR already described for M. avium and M. intracellulare, MIRU 3 (Bull at al.), was polymorphic with different allele sizes. None of the new MIRU-VNTR identified from the strain M. avium 104 could be validated on our set of 10 isolates of M. intracellulare.

Consequently, of the 45 candidate MIRU-VNTR only seven, MIRU 3 (Bull et al.), MIN 18, MIN 19, MIN 20, MIN 22, MIN 31, and MIN 33, were present and exhibited polymorphism. The stability of the seven polymorphic MIRU-VNTR markers pheromone was studied on four isolates. No difference was seen in the gel profiles before and after 10 passages in MGIT medium. Thus, an MIRU-VNTR scheme was proposed, including seven markers. It allowed unambiguous type assignment using agarose gels, with PCR products ranging in size between 200 and 750 bp. Characteristics of each MIRU-VNTR marker are shown in Table 1. As the genome sequence of M. intracellulare was available only in a contig format and was not annotated, it was impossible to determine where the MIRU-VNTR were located in the genome. The sizes of the unit repeat ranged from 53 to 57 bp. Sequencing of the different size PCR products at each of the seven loci from each of the 10 isolates confirmed the sizes and sequences of individual MIRU-VNTR loci.

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