Abstract
This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441 bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.
| Original language | English |
|---|---|
| Pages (from-to) | 399-408 |
| Number of pages | 10 |
| Journal | Molecular and Cellular Probes |
| Volume | 18 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Dec 2004 |
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Keywords
- DNA sequencing
- HPLC
- Non-tuberculous mycobacteria
- PCR-restriction analysis
- Phylogeny
- Taxonomy
ASJC Scopus subject areas
- Cell Biology
- Molecular Biology
Cite this
Taxonomic and phylogenetic status of non-tuberculous mycobacteria in a Caribbean setting. / Ferdinand, Séverine; Legrand, Eric; Goh, Khye Seng; Berchel, Mylène; Mazzarelli, Gianna; Sola, Christophe; Tortoli, Enrico; Rastogi, Nalin.
In: Molecular and Cellular Probes, Vol. 18, No. 6, 12.2004, p. 399-408.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Taxonomic and phylogenetic status of non-tuberculous mycobacteria in a Caribbean setting
AU - Ferdinand, Séverine
AU - Legrand, Eric
AU - Goh, Khye Seng
AU - Berchel, Mylène
AU - Mazzarelli, Gianna
AU - Sola, Christophe
AU - Tortoli, Enrico
AU - Rastogi, Nalin
PY - 2004/12
Y1 - 2004/12
N2 - This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441 bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.
AB - This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441 bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.
KW - DNA sequencing
KW - HPLC
KW - Non-tuberculous mycobacteria
KW - PCR-restriction analysis
KW - Phylogeny
KW - Taxonomy
UR - http://www.scopus.com/inward/record.url?scp=5644261182&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=5644261182&partnerID=8YFLogxK
U2 - 10.1016/j.mcp.2004.06.006
DO - 10.1016/j.mcp.2004.06.006
M3 - Article
C2 - 15488380
AN - SCOPUS:5644261182
VL - 18
SP - 399
EP - 408
JO - Molecular and Cellular Probes
JF - Molecular and Cellular Probes
SN - 0890-8508
IS - 6
ER -