Diversity of environmental Mycobacterium isolates from hemodialysis water as shown by a multigene sequencing approach

Abstract

Here we used a multigene sequencing approach for the identification and molecular typing of environmental mycobacteria of the fast-growing subgroup. Strains were isolated from hemodialysis water and clinical samples. Eleven type strains of related species of the genus were also included in this study. To gain further insight into the diversity of the environmental mycobacteria, we analyzed several housekeeping genes (16S rRNA, ITS1, gyrB, hsp65, recA, rpoB, and sodA). No individual phylogenetic tree allowed good discrimination of all of the species studied. However, a concatenated and a consensus analysis, combining the genes, allowed better discrimination of each strain to the species level, and the increase in sequence size also led to greater tree robustness. This approach is useful not only for the discrimination and identification of environmental mycobacteria but also for their molecular typing and studies of population genetics. Our results demonstrate high genetic diversity among the isolates obtained, which are probably new species of the genus.

FIG. 1.

Phylogenetic tree based on the 16S rRNA gene sequences of the environmental and clinical Mycobacterium strains studied. The bar indicates sequence divergence. Bootstrap values of 500 or more (from 1,000 replicates) are indicated at the nodes. Sequence accession numbers are in parentheses. Roman numerals indicate phylogenetic groupings.

FIG. 2.

Hypothetical multilocus concatenated tree showing the molecular evolutionary relationships of the gyrB, hsp65, recA, rpoB, sodA, and 16S rRNA genes of the environmental and clinical Mycobacterium strains studied. The bar indicates sequence divergence. Bootstrap values of 500 or more (from 1,000 replicates) are indicated at the nodes. Roman numerals indicate phylogenetic groupings in the 16S rRNA gene analysis.

FIG. 3.

Hypothetical multilocus consensus tree showing the molecular evolutionary relationships of the gyrB, hsp65, recA, rpoB, sodA, and 16S rRNA genes of the environmental and clinical Mycobacterium strains studied. The bar indicates sequence divergence. Roman numerals indicate phylogenetic groupings in the 16S rRNA gene analysis.

FIG. 4.

Splits tree showing the distribution of all of the environmental and clinical isolates studied, as well as the closely related type strains (A). (B) Detail of the group I network.