A polymorphic region was discovered in the genetically uncharacterized opportunistic pathogen Mycobacterium abscessus. The region contains a novel 17 kb insertion sequence (IS) named ISMab1. ISMab1 contains two complete ORFs and one partial ORF located in segments with over 80 % nucleotide identity to Mycobacterium avium IS1601 and IS999 and to previously unreported IS-like elements from Mycobacterium smegmatis. The marked similarity within this family of elements is supportive of horizontal transfer between environmental mycobacterial species. In clinical isolates, ISMab1 was either present as a single copy or absent. The polymorphic region containing ISMab1 was identified by genomic subtraction between a parental strain and phenotypic variant. The variant has a 142 kb genomic deletion and this is flanked in the parental strain by complex arrays of inverted and direct repeats. Clinical isolates of M. abscessus were probed for the deletion and flanking sequences and two were found to be missing more than 20 kb. No regional deletions were found in the type strain, ATCC 19977. Although M. abscessus is a rapidly growing species, comparative sequence analysis of 23 kb from the polymorphic region showed that most local ORFs have greater amino acid identity to proteins encoded by genes from the slowly growing mycobacteria, M. avium and Mycobacterium tuberculosis, than to the rapid-grower M. smegmatis. Several ORFs also have strong similarity to Pseudomonas aeruginosa genes with a potential role in β-oxidation.Keywords : rapidly growing mycobacteria, insertion element, horizontal transfer, genetic variation
INTRODUCTIONThe genus Mycobacterium has been divided into two groups on the basis of growth rate and, in general, this division is supported by phylogenetic analyses of the 16S rRNA gene (Pitulle et al., 1992). The major pathogens Mycobacterium leprae, the Mycobacterium tuberculosis complex and Mycobacterium avium complex, are members of the slowly growing mycobacteria. The second group, the rapidly growing mycobacteria (RGM), in- Abbreviations : DR, direct repeat ; IR, inverted repeat ; IS, insertion sequence ; RGM, rapidly growing mycobacteria.The GenBank accession number for the sequence reported in this paper is AF513500.cludes saprophytic species found in soil and water systems (Falkinham, 1996 ;Howard & Byrd, 2000). Comparative analysis of 16S rRNA gene sequences indicates that the RGM may be the phylogenetically older group (Pitulle et al., 1992).Several species of RGM, particularly Mycobacterium abscessus, Mycobacterium chelonae and Mycobacterium fortuitum, are opportunistic pathogens and can cause infections ranging from localized abscesses to pulmonary and disseminated disease (Griffith et al., 1993 ;Howard & Byrd, 2000 ;Wright & Wallace, 1995). RGM-associated disease tends to be sporadic and usually associated with injury or surgical procedures (Wright & Wallace, 1995). However, large outbreaks of post-operative wound infections (Chadha et al., 1998) and post-injection abscesses (Galil et al., 1999 ; Vill...