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.

Genetic and functional heterogeneities among fluorescent Pseudomonas isolated from environmental samples

“…In most cases, different species show very similar or identical 16S rDNA sequences (Grimont, 2002;Gomila et al, 2007). In our study, identifi cation of some isolates has to be confi rmed due to the controversial information in databases and in some instance equal identity in 16S rDNA sequence was shared with more than one species.…”

Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil

“…The rpoB amplification was performed using primers MycoF and MycoR, as described by Adékambi et al (2003). Two primers described in previous publications (Adékambi & Drancourt 2004, Gomila et al 2007 were used for the amplification and sequencing of the 3' region of the 16S rDNA. The gyrB amplification primers were designed based on the sequence of the M. abscessus ATCC 19977 genome (GenBank accession NC_010397).…”

“…PRA-16S -For the PRA-16S determinations, the primers 800F (Adékambi & Drancourt 2004) and 16R1492 (Gomila et al 2007) were used to amplify a 733 bp fragment. The same reagents, volumes and amplification conditions described above were used in the 16S rDNA PCR with the exception of changes in the MgCl 2 concentration (1.5 mM final concentration) and the annealing temperature (60ºC).…”

Mycobacterium alsense sp. nov., a scotochromogenic slow grower isolated from clinical respiratory specimens

“…The regions investigated included the almost-complete 16S rRNA gene (Kirschner et al, 1993), the complete internal transcribed spacer between 16S and 23S rRNA (ITS1) (Roth et al, 1998), and parts of genes encoding 65 kDa heat-shock protein (hsp65) (McNabb et al, 2006), RNA polymerase b subunit (rpoB) (Adékambi et al, 2003), RNA polymerase b' subunit (rpoBC) (Dai et al, 2011), superoxide dismutase (sodA) (Zolg & Philippi-Schulz, 1994), DNA gyrase b subunit (gyrB) (Gomila et al, 2007), molecular chaperone DnaK (dnaK) and preprotein translocase subunit secA (secA1) (Dai et al, 2011). Microheterogeneity was detected in seven genetic targets with the strains presenting the same sequence in 16S rRNA and ITS1 only (Table 1).…”