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A polymorphic region in Mycobacterium abscessus contains a novel insertion sequence element^b

University of New Mexico School of Medicine, Dept of Internal Medicine, 915 Camino de Salud, Albuquerque, NM 87131, USA¹
Department of Medicine, Albuquerque Veterans Affairs Medical Center, 1501 San Pedro SE, Albuquerque, NM 87108, USA²
UNM Health Science Center Cancer Research and Treatment Center, 900 Camino de Salud, Albuquerque, NM 87131, USA³

Author for correspondence: C. Richard Lyons. Tel: +1 505 272 4450. Fax: +1 505 272 9912. e-mail: clyons{at}salud.unm.edu

A polymorphic region was discovered in the genetically uncharacterized opportunistic pathogen Mycobacterium abscessus. The region contains a novel 1·7 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 14·2 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 ß-oxidation.

Keywords: rapidly growing mycobacteria, insertion element, horizontal transfer, genetic variation

Abbreviations: DR, direct repeat; IR, inverted repeat; IS, insertion sequence; RGM, rapidly growing mycobacteria

^b The GenBank accession number for the sequence reported in this paper is AF513500.

^a Present address: Center for Pulmonary and Infectious Disease Control, The University of Texas Health Center at Tyler, Tyler, TX 75708-3154, USA.

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