A novel insertion sequence, IS1642, of Mycobacterium avium, which forms long direct repeats of variable length.

A new insertion sequence (IS), IS1642, was identified in a Mycobacterium avium strain isolated from a human patient. IS1642 had a size of 1642 bp and contained a single ORF encoding a probable transposase of 503 amino acid residues homologous (79% identity) to that of IS1549 found in Mycobacterium smegmatis. The IS1642 included imperfect inverted repeats (5'-cctgacttttatca-3', 5'-tgataaaagtcggg-3') on its ends, and was flanked by direct repeats of variable length ranging from 5 to 161 bp. It was suggested that the IS1642 was widely distributed in many M. avium strains of human patients, and the Southern blot profile of IS1642 was very diverse among the strains examined. The transposition event of IS1642 was observed by in vitro repeated passages, showing that the IS1642 is actually a transposable element. In light of these characteristics, IS1642 could be a new useful marker when genotyping with high discrimination is required.