| Extended Bibliography: |
Show bibliography
| Ref #: |
60196 |
| Author(s): |
Kim,B.J.;Lee,S.H.;Lyu,M.A.;Kim,S.J.;Bai,G.H.;Chae,G.T.;Kim,E.C.;Cha,C.Y.;Kook,Y.H. |
| Journal: |
J Clin Microbiol |
| Title: |
Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB) |
| Volume: |
37 |
| Page(s): |
1714-20 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AF057449
GENBANK/AF057450
GENBANK/AF057451
GENBANK/AF057452
GENBANK/AF057453
GENBANK/AF057454
GENBANK/AF057455
GENBANK/AF057456
GENBANK/AF057457
GENBANK/AF057458
GENBANK/AF057459
GENBANK/AF057460
GENBANK/AF057461
GENBANK/AF057462
GENBANK/AF057463
GENBANK/AF057464
GENBANK/AF057465
GENBANK/AF057466
GENBANK/AF057467
GENBANK/AF057468
GENBANK/AF057469
GENBANK/AF057470
GENBANK/AF057471
GENBANK/AF057472
GENBANK/AF057473
GENBANK/AF057474
GENBANK/AF057475
GENBANK/AF057476
GENBANK/AF057477
GENBANK/AF057478
etc.
Amino Acid Sequence
DNA-Directed RNA Polymerases/chemistry/*genetics
Humans
Molecular Sequence Data
Mycobacterium/*classification/enzymology/genetics
Mycobacterium Infections/microbiology
Phylogeny
Restriction Mapping
Sequence Alignment
Sequence Homology, Amino Acid
|
| Remarks: |
For the differentiation and identification of mycobacterial species, the rpoB gene, encoding the beta subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 44 reference strains of mycobacteria and clinical isolates (107 strains) by PCR. The nucleotide sequences were directly determined (306 bp) and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genus Mycobacterium. Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. Pathogenic Mycobacterium kansasii was easily differentiated from nonpathogenic M. gastri; this differentiation cannot be achieved by using 16S rRNA gene (rDNA) sequences. By being grouped into species-specific clusters with low-level sequence divergence among strains of the same species, all of the clinical isolates could be easily identified. These results suggest that comparative sequence analysis of amplified rpoB DNAs can be used efficiently to identify clinical isolates of mycobacteria in parallel with traditional culture methods and as a supplement to 16S rDNA gene analysis. Furthermore, in the case of M. tuberculosis, rifampin resistance can be simultaneously determined. |
| URL: |
10325313 |
|
| Ref #: |
75210 |
| Author(s): |
Stone,B.B.;Nietupski,R.M.;Breton,G.L.;Weisburg,W.G. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Comparison of Mycobacterium 23S rRNA sequences by high-temperature reverse transcription and PCR |
| Volume: |
45 |
| Page(s): |
811-9 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/U24502
GENBANK/U24503
GENBANK/U24504
GENBANK/U24505
GENBANK/U24506
GENBANK/U24507
GENBANK/U24508
GENBANK/U24509
GENBANK/U24510
GENBANK/U24511
GENBANK/U24512
GENBANK/U24513
GENBANK/U24514
GENBANK/U24515
GENBANK/U24516
GENBANK/U24517
GENBANK/U24518
GENBANK/U24519
GENBANK/U24520
GENBANK/U24521
GENBANK/U24522
GENBANK/U24523
GENBANK/U24524
GENBANK/U24525
GENBANK/U24526
GENBANK/U24527
GENBANK/U24528
GENBANK/U24529
GENBANK/U24530
GENBANK/U24531
Base Sequence
Molecular Sequence Data
Mycobacterium/*genetics
Phylogeny
*Polymerase Chain Reaction
RNA, Bacterial/*chemistry
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/*chemistry
Temperature
Transcription, Genetic
|
| Remarks: |
We describe a modified rRNA sequence analysis method which we used to determine the phylogenetic relationships among 58 species belonging to the genus Mycobacterium. We combined the sensitivity of the reverse transcriptase PCR for amplifying nanogram amounts of template rRNA material with the elevated extension temperatures used for the thermostable DNA polymerase from Thermus thermophilus. A 70 degrees C reverse transcription extension step permitted improved read-through of highly structured rRNA templates from members of the genus Mycobacterium, which have G+C contents of 66 to 71 mol%. The nucleic acid sequences of the amplified material were then determined by performing thermal cycle sequencing with alpha-33P-labeled primers, again with extension at 70 degrees C. Nonspecifically terminated bands were chased by using terminal deoxynucleotidyl transferase. Our method had a template requirement of nanogram amounts or less of purified RNA or 2,000 CFU of intact cells and had sufficient sensitivity so that lyophils obtained from the American Type Culture Collection could be used as source material. Sequences from a 250-nucleotide stretch of the 23S rRNA were aligned, and phylogenetic trees were evaluated by using the De Soete distance treeing algorithm and Rhodococcus bronchialis as the outgroup. Our 23S rRNA trees were compared with previously published 16S rRNA trees, including the comprehensive trees developed by the University of Illinois Ribosomal Database Project, and included 15 species not evaluated previously. Most of the groups were in general agreement and were consistent with relationships determined on the basis of biochemical characteristics, but some new relationships were also observed. |
| URL: |
7547304 |
|
| Ref #: |
95496 |
| Author(s): |
Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A. |
| Journal: |
J Clin Microbiol |
| Title: |
Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species |
| Volume: |
39 |
| Page(s): |
3637-48 |
| Year: |
2001 |
| Keyword(s): |
*Databases, Nucleic Acid
*Genes, rRNA
Humans
Internet
Mycobacterium/*classification/genetics
Mycobacterium Infections/*microbiology
Phylogeny
Quality Control
RNA, Ribosomal, 16S/*genetics
Reference Standards
*Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species. |
| URL: |
11574585 |
|
| Ref #: |
59414 |
| Author(s): |
Pitulle,C.;Dorsch,M.;Kazda,J.;Wolters,J.;Stackebrandt,E. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogeny of rapidly growing members of the genus Mycobacterium |
| Volume: |
42 |
| Page(s): |
337-43 |
| Year: |
1992 |
| Keyword(s): |
GENBANK/X55593
GENBANK/X55594
GENBANK/X55595
GENBANK/X55596
GENBANK/X55597
GENBANK/X55598
GENBANK/X55599
GENBANK/X55600
GENBANK/X55601
GENBANK/X55602
Base Sequence
Molecular Sequence Data
Mycobacteria, Atypical/classification/*genetics
Mycobacterium/classification/*genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Homology, Nucleic Acid
|
| Remarks: |
The 16S rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16S rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaurum and M. diernhoferi, (ii) M. gadium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. flavescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses. |
| URL: |
1380284 |
|
| Ref #: |
13155 |
| Author(s): |
Pitulle,C.;Dorsch,M.;Kazda,J.;Wolters,J.;Stackebrandt,E. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogeny of rapidly growing members of the genus Mycobacterium |
| Volume: |
42 |
| Page(s): |
337-43 |
| Year: |
1992 |
| Keyword(s): |
GENBANK/X55593
GENBANK/X55594
GENBANK/X55595
GENBANK/X55596
GENBANK/X55597
GENBANK/X55598
GENBANK/X55599
GENBANK/X55600
GENBANK/X55601
GENBANK/X55602
Base Sequence
Molecular Sequence Data
Mycobacteria, Atypical/classification/*genetics
Mycobacterium/classification/*genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Homology, Nucleic Acid
Support, Non-U.S. Gov't
|
| Remarks: |
The 16S rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16S rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaurum and M. diernhoferi, (ii) M. gadium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. flavescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses. |
| URL: |
92368931 |
|
| Ref #: |
13151 |
| Author(s): |
Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A. |
| Journal: |
J Clin Microbiol |
| Title: |
Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species |
| Volume: |
39 |
| Page(s): |
3637-48 |
| Year: |
2001 |
| Keyword(s): |
*Databases, Nucleic Acid
*Genes, rRNA
Human
Internet
Mycobacterium/*classification/genetics
Mycobacterium Infections/*microbiology
Phylogeny
Quality Control
RNA, Ribosomal, 16S/*genetics
Reference Standards
*Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species. |
| URL: |
21458757 |
|
|
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