| Extended Bibliography: |
Show bibliography
| Ref #: |
95518 |
| Author(s): |
Gingeras,T.R.;Ghandour,G.;Wang,E.;Berno,A.;Small,P.M.;Drobniewski,F.;Alland,D.;Desmond,E.;Holodniy,M.;Drenkow,J. |
| Journal: |
Genome Res |
| Title: |
Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays |
| Volume: |
8 |
| Page(s): |
435-48 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/AF059766
GENBANK/AF059767
GENBANK/AF059768
GENBANK/AF059769
GENBANK/AF059770
GENBANK/AF059771
GENBANK/AF059772
GENBANK/AF059773
GENBANK/AF059774
GENBANK/AF059775
GENBANK/AF059776
GENBANK/AF059777
GENBANK/AF059778
GENBANK/AF059779
GENBANK/AF059780
GENBANK/AF059781
GENBANK/AF059782
GENBANK/AF059783
GENBANK/AF059784
GENBANK/AF059785
GENBANK/AF059786
GENBANK/AF059787
GENBANK/AF059788
GENBANK/AF059789
GENBANK/AF059790
GENBANK/AF059791
GENBANK/AF059792
GENBANK/AF059793
GENBANK/AF059794
GENBANK/AF059795
Alleles
DNA, Bacterial/*analysis
DNA-Directed RNA Polymerases/genetics
Drug Resistance, Microbial/genetics
Gene Frequency
Genes, Bacterial
Genotype
Molecular Sequence Data
Mutagenesis
Mycobacterium/drug effects/*genetics/*isolation & purification
Mycobacterium tuberculosis/drug effects/genetics
Nucleic Acid Hybridization/methods
Oligonucleotides/analysis
Polymorphism, Genetic
RNA, Ribosomal, 16S/genetics
Rifampin/pharmacology
Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of the rpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis. The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 16S genes and by analysis of the rpoB oligonucleotide array hybridization patterns. Species identification for each of the isolates was similar irrespective of whether 16S sequence, rpoB sequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S and rpoB gene sequences provided discordant estimates of the genetic diversity within a species. In addition to confirming the array's intended utility for sequencing the region of M. tuberculosis that confers rifampin resistance, this work demonstrates that this array can identify the species of nontuberculous Mycobacteria. This demonstrates the general point that DNA microarrays that sequence important genomic regions (such as drug resistance or pathogenicity islands) can simultaneously identify species and provide some insight into the organism's population structure. |
| URL: |
9582189 |
|
| 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 #: |
61936 |
| Author(s): |
Lefmann,M.;Honisch,C.;Bocker,S.;Storm,N.;von Wintzingerode,F.;Schlotelburg,C.;Moter,A.;van den Boom,D.;Gobel,U.B. |
| Journal: |
J Clin Microbiol |
| Title: |
Novel mass spectrometry-based tool for genotypic identification of mycobacteria |
| Volume: |
42 |
| Page(s): |
339-46 |
| Year: |
2004 |
| Keyword(s): |
Genotype
Mycobacterium/classification/*genetics
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods
|
| Remarks: |
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for the identification of mycobacteria. Full-length 16S rDNA reference sequences of 12 type strains of Mycobacterium spp. frequently isolated from clinical specimens were determined by PCR, cloning, and sequencing. For MALDI-TOF MS-based comparative sequence analysis, mycobacterial 16S rDNA signature sequences ( approximately 500 bp) of the 12 type strains and 24 clinical isolates were PCR amplified using RNA promoter-tagged forward primers. T7 RNA polymerase-mediated transcription of forward strands in the presence of 5-methyl ribo-CTP maximized mass differences of fragments generated by base-specific cleavage. In vitro transcripts were subsequently treated with RNase T1, resulting in G-specific cleavage. Sample analysis by MALDI-TOF MS showed a specific mass signal pattern for each of the 12 type strains, allowing unambiguous identification. All 24 clinical isolates were identified unequivocally by comparing their detected mass signal pattern to the reference sequence-derived in silico pattern of the type strains and to the in silico mass patterns of published 16S rDNA sequences. A 16S rDNA microheterogeneity of the Mycobacterium xenopi type strain (DSM 43995) was detected by MALDI-TOF MS and later confirmed by Sanger dideoxy sequencing. In conclusion, analysis of 16S rDNA amplicons by MS after base-specific cleavage of RNA transcripts allowed fast and reliable identification of the Mycobacterium tuberculosis complex and ubiquitous mycobacteria (mycobacteria other than tuberculosis). The technology delivers an open platform for high-throughput microbial identification on the basis of any specific genotypic marker region. |
| URL: |
14715774 |
|
| 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 |
|
| Ref #: |
4493 |
| Journal: |
Int. J. Syst. Bacteriol. |
| Volume: |
19 |
| Page(s): |
260 |
| Year: |
1969 |
|
| Ref #: |
4494 |
| Author(s): |
Prissick,F.H.;Masson,A.M. |
| Journal: |
Can. Med. Assoc. J. |
| Title: |
Cervical lymphadenitis in children caused by chromogenic mycobacteria. |
| Volume: |
75 |
| Page(s): |
798-803 |
| Year: |
1956 |
|
| Ref #: |
4495 |
| Author(s): |
Prissick,F.H.;Masson,A.M. |
| Journal: |
Can. J. Microbiol. |
| Title: |
Yellow-pigmented pathogenic mycobacteria from cervical lymphodenitis. |
| Volume: |
3 |
| Page(s): |
91-100 |
| Year: |
1957 |
|
| Ref #: |
6924 |
| Author(s): |
DeutschesInstitutfürNormungDIN.NormenausschußMedizin(NAMed) |
| Title: |
DIN 58959-7. Qualitätsmanagement in der medizinischen Mikrobiologie. Teil 7: Allgemeine Anforderungen an das Mitführen von Kontrollstämmen. Beiblatt 2: ATCC- und DSM-Nummern häufig verwendeter Kontrollstämme. |
| Year: |
1997 |
|
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