Molecular characterization of environmental Mycobacteriumstrains by PCR-restriction fragment length polymorphism of hsp65and by sequencing of hsp65, and of 16S and ITS1 rDNA

Abstract

Fifteen mycobacterial strains from the environment, not clearly identifiable by biochemical properties, were analyzed with molecular markers: PCR-restriction enzyme analysis of hsp65 and sequencing of hsp65, and of the internal transcribed spacer 1 (ITS1) and 16S rDNA. The 16S rDNA sequencing closely related the strains to a slow-growing mycobacterial group including Mycobacterium simiae, Mycobacterium lentiflavum, Mycobacterium genavense, Mycobacterium triplex and Mycobacterium heidelbergense. A stretch of T bases at the level of 16S rDNA enabled the separation of M. simiae and M. lentiflavum from M. genavense, M. triplex and M. heidelbergense; hence the attribution of some environmental strains to the first or second group. But the distances between the two clades were very short and the relative positions of environmental strains and of reference strains were not resolved in terms of node robustness (low bootstrap values) in the distance tree. However, the hsp65 restriction profiles suggested assigning six strains to the M. lentiflavum species, although these strains had been found closely related to M. genavense and M. triplex from 16S rDNA nucleotide signatures. The clustering of environmental strains into the same three clusters was deduced from analysis of three sequence data ( hsp65, and ITS1 and 16S rDNA), but the taxonomic affiliation of environmental strains to reference strains remained tentative. Among environmental strains and reference strains, the distances found from hsp65 sequences had the same amplitude as those found between different strains of Mycobacterium gordonae. From ITS1 rDNA sequences, the distances found between the strains of the Mycobacterium avium complex also had the same amplitude as those found between environmental strains and reference strains. From our results, it appears that the environmental strains and the reference strains could constitute a complex of subspecies or closely related species. Their taxonomic status must be confirmed by DNA/DNA hybridization experiments.