| Extended Bibliography: |
Show bibliography
| Ref #: |
61112 |
| Author(s): |
Springer,B.;Bottger,E.C.;Kirschner,P.;Wallace RJ,J.r. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacterium mucogenicum sp. nov |
| Volume: |
45 |
| Page(s): |
262-7 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X80771
GENBANK/X80772
GENBANK/X80773
GENBANK/X82235
GENBANK/X82236
Base Sequence
DNA, Bacterial/*genetics
Genes, Bacterial
Humans
Molecular Sequence Data
Mycobacterium/*classification/genetics/physiology
Mycobacterium chelonae/classification/genetics
Phylogeny
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
Sequence Analysis
Sequence Homology, Nucleic Acid
Water Microbiology
|
| Remarks: |
The Mycobacterium chelonae-like organism (MCLO) is a recently described member of the Mycobacterium fortuitum complex which causes posttraumatic skin infections and catheter sepsis. This taxon is a distinct group biochemically and has a unique mycolic acid profile as determined by high-performance liquid chromatography. Its phylogenetic relationships to other mycobacteria, however, have not been studied previously. We sequenced 1,062 bp of the 16S rRNA genes from three MCLO strains obtained from the American Type Culture Collection and compared our results with the sequences of previously described taxa of rapidly growing and slowly growing mycobacteria. Two biochemically typical strains (ATCC 49650T [T = type strain] and ATCC 49651) had identical sequences, while the sequence of a biochemically atypical strain (ATCC 49649) differed by 4 bp from the sequence of the two typical strains. The Hamming distances between these MCLO strains and related rapidly growing mycobacteria are comparable to the Hamming distances among taxa of rapidly growing mycobacteria established as species by DNA-DNA hybridization. We propose the name Mycobacterium mucogenicum sp. nov. for this new taxon because of the highly mucoid nature of most isolates on solid media. |
| URL: |
7537060 |
|
| 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 #: |
60037 |
| Author(s): |
Hamid,M.E.;Roth,A.;Landt,O.;Kroppenstedt,R.M.;Goodfellow,M.;Mauch,H. |
| Journal: |
J Clin Microbiol |
| Title: |
Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense strains based on 16S-23S ribosomal DNA internal transcribed spacer sequences |
| Volume: |
40 |
| Page(s): |
707-11 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AJ291580
GENBANK/AJ291581
GENBANK/AJ291582
GENBANK/AJ291583
GENBANK/AJ291584
GENBANK/AJ291585
GENBANK/AJ291586
GENBANK/AJ291587
GENBANK/AJ291588
GENBANK/AJ291589
GENBANK/AJ291590
GENBANK/AJ291591
GENBANK/AJ291592
GENBANK/AJ291593
GENBANK/AJ291594
GENBANK/AJ291595
GENBANK/AJ291596
GENBANK/AJ291597
GENBANK/AJ291598
GENBANK/AJ291599
GENBANK/AJ291600
GENBANK/Y10384
GENBANK/Y10385
GENBANK/Y11581
GENBANK/Y11582
Animals
Base Sequence
Cattle
Cattle Diseases/*microbiology
DNA, Ribosomal Spacer/*genetics
Molecular Sequence Data
Mycobacterium/*classification/genetics
Mycobacterium Infections/microbiology/*veterinary
Phylogeny
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
Sequence Analysis, DNA
|
| Remarks: |
16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA sequence analyses were performed on Mycobacterium farcinogenes and M. senegalense strains and 26 strains of other rapidly growing mycobacteria to investigate the phylogenetic structure of bovine farcy mycobacteria within the M. fortuitum complex. M. farcinogenes and M. senegalense were indistinguishable in their 5"-end 16S rDNA but showed both considerable interspecies spacer sequence divergence and a high level of intraspecies sequence stability. A rapid detection assay using PCR and hybridization with species-specific probes was developed. The assay was specific among 46 species other than M. farcinogenes and M. senegalense and correctly identified all M. farcinogenes and M. senegalense strains. PCR- and 16S-23S rDNA sequence-based detection will be a valuable approach for diagnosis of the causal agents of African bovine farcy in cattle. |
| URL: |
11826003 |
|
| 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 #: |
61305 |
| Author(s): |
Gonzalez-y-Merchand,J.A.;Garcia,M.J.;Gonzalez-Rico,S.;Colston,M.J.;Cox,R.A. |
| Journal: |
J Bacteriol |
| Title: |
Strategies used by pathogenic and nonpathogenic mycobacteria to synthesize rRNA |
| Volume: |
179 |
| Page(s): |
6949-58 |
| Year: |
1997 |
| Keyword(s): |
GENBANK/X99775
GENBANK/X99776
GENBANK/X99777
GENBANK/Y13910
GENBANK/Y13911
Base Sequence
Chromosome Mapping
Cloning, Molecular
DNA, Bacterial/genetics
Gene Expression Regulation, Bacterial
Genes, Bacterial
Genome, Bacterial
Molecular Sequence Data
Molecular Structure
Mycobacterium/*genetics/*metabolism/pathogenicity
Mycobacterium chelonae/genetics/metabolism/pathogenicity
Mycobacterium fortuitum/genetics/metabolism/pathogenicity
Mycobacterium phlei/genetics/metabolism/pathogenicity
Plasmids
Polymerase Chain Reaction
*Promoter Regions (Genetics)
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal/chemistry/metabolism
RNA, Ribosomal, 16S/genetics
Ribosomes/*metabolism
Sequence Alignment
Sequence Analysis, DNA
Transcription, Genetic
Virulence/genetics
*rRNA Operon
|
| Remarks: |
One rRNA operon of all mycobacteria studied so far is located downstream from a gene thought to code for the enzyme UDP-N-acetylglucosamine carboxyvinyl transferase (UNAcGCT), which is important to cell wall synthesis. This operon has been designated rrnAf for fast-growing mycobacteria and rrnAs for slow growers. We have investigated the upstream sequences and promoter activities of rrnA operons of typical fast growers which also possess a second rrn (rrnBf) operon and of the rrnA operons of the fast growers Mycobacterium abscessus and Mycobacterium chelonae, which each have a single rrn operon per genome. These fast growers have a common strategy for increasing the efficiency of transcription of their rrnA operons, thereby increasing the cells' potential for ribosome synthesis. This strategy involves the use of multiple (three to five) promoters which may have arisen through successive duplication events. Thus we have identified a hypervariable multiple promoter region (HMPR) located between the UNAcGCT gene and the 16S rRNA coding region. Two promoters, P1 and PCL1, appear to play pivotal roles in mycobacterial rRNA synthesis; they are present in all of the species examined and are the only promoters used for rRNA synthesis by the pathogenic slow growers. P1 is located within the coding region of the UNAcGCT gene, and PCL1 has a characteristic sequence that is related to but distinct from that of the additional promoters. In fast-growing species, P1 and PCL1 produce less than 10% of rRNA transcripts, so the additional promoters found in the HMPR are important in increasing the potential for rRNA synthesis during rapid growth. In contrast, rrnB operons appear to be regulated by a single promoter; because less divergence has taken place, rrnB appears to be younger than rrnA. |
| URL: |
9371439 |
|
| Ref #: |
59154 |
| Author(s): |
Khan,I.U.;Selvaraju,S.B.;Yadav,J.S. |
| Journal: |
J Clin Microbiol |
| Title: |
Method for rapid identification and differentiation of the species of the Mycobacterium chelonae complex based on 16S-23S rRNA gene internal transcribed spacer PCR-restriction analysis |
| Volume: |
43 |
| Page(s): |
4466-72 |
| Year: |
2005 |
| Keyword(s): |
GENBANK/AY497531
GENBANK/AY498739
GENBANK/AY498740
*Bacterial Typing Techniques
Base Sequence
DNA, Bacterial/analysis
DNA, Ribosomal Spacer/*analysis
Genes, rRNA
Humans
Molecular Sequence Data
Mycobacteria, Atypical/*classification/genetics
Mycobacterium chelonae/*classification/genetics
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/genetics
Restriction Mapping/*methods
Time Factors
|
| Remarks: |
Members of the Mycobacterium chelonae complex (MCC), including M. immunogenum, M. chelonae, and M. abscessus, have been associated with nosocomial infections and occupational hypersensitivity pneumonitis due to metalworking fluid (MWF) exposures. In order to minimize these health hazards, an effective and rapid assay for detection of MCC species and differentiation of MCC species from other species of rapidly growing mycobacteria (RGM) and from one another is warranted. Here we report such a method, based on the variable 16S-23S rRNA gene internal transcribed spacer (ITS) region. Mycobacterium genus-specific primers derived from highly conserved sequences in the ITS region and the flanking 16S rRNA gene were used. Specificity of the primers was verified using the MCC member species, 11 non-MCC RGM species, 3 slow-growing mycobacterial (SGM) species (two strains each), and 19 field isolates, including 18 MCC isolates (from in-use MWF) and one non-MCC isolate (from reverse osmosis water). The ITS amplicon size of M. immunogenum varied from those of M. chelonae and M. abscessus. Sequencing of the approximately 250-bp-long ITS amplicons of the three MCC member species showed differences in 24 to 34 bases, thereby yielding variable deduced restriction maps. ITS PCR-restriction analysis using the in silico-selected restriction enzyme MaeII or HphI differentiated the three MCC members from one another and from other RGM and SGM species without sequencing. The enzyme MaeII discriminated all three member species; however, HphI could only differentiate M. immunogenum from M. chelonae and M. abscessus. Use of an optimized rapid DNA template preparation step based on direct cell lysis in the PCR tube added to the simplicity and adaptability of the developed assay. |
| URL: |
16145093 |
|
| Ref #: |
13153 |
| Author(s): |
Springer,B.;Bottger,E.C.;Kirschner,P.;Wallace RJ,J.r. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacterium mucogenicum sp. nov |
| Volume: |
45 |
| Page(s): |
262-7 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X80771
GENBANK/X80772
GENBANK/X80773
GENBANK/X82235
GENBANK/X82236
Base Sequence
DNA, Bacterial/*genetics
Genes, Bacterial
Human
Molecular Sequence Data
Mycobacterium/*classification/genetics/physiology
Mycobacterium chelonae/classification/genetics
Phylogeny
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
Sequence Analysis
Sequence Homology, Nucleic Acid
Water Microbiology
|
| Remarks: |
The Mycobacterium chelonae-like organism (MCLO) is a recently described member of the Mycobacterium fortuitum complex which causes posttraumatic skin infections and catheter sepsis. This taxon is a distinct group biochemically and has a unique mycolic acid profile as determined by high-performance liquid chromatography. Its phylogenetic relationships to other mycobacteria, however, have not been studied previously. We sequenced 1,062 bp of the 16S rRNA genes from three MCLO strains obtained from the American Type Culture Collection and compared our results with the sequences of previously described taxa of rapidly growing and slowly growing mycobacteria. Two biochemically typical strains (ATCC 49650T [T = type strain] and ATCC 49651) had identical sequences, while the sequence of a biochemically atypical strain (ATCC 49649) differed by 4 bp from the sequence of the two typical strains. The Hamming distances between these MCLO strains and related rapidly growing mycobacteria are comparable to the Hamming distances among taxa of rapidly growing mycobacteria established as species by DNA-DNA hybridization. We propose the name Mycobacterium mucogenicum sp. nov. for this new taxon because of the highly mucoid nature of most isolates on solid media. |
| URL: |
95244308 |
|
| Ref #: |
13152 |
| Author(s): |
Gonzalez-y-Merchand,J.A.;Garcia,M.J.;Gonzalez-Rico,S.;Colston,M.J.;Cox,R.A. |
| Journal: |
J Bacteriol |
| Title: |
Strategies used by pathogenic and nonpathogenic mycobacteria to synthesize rRNA |
| Volume: |
179 |
| Page(s): |
6949-58 |
| Year: |
1997 |
| Keyword(s): |
GENBANK/X99775
GENBANK/X99776
GENBANK/X99777
GENBANK/Y13910
GENBANK/Y13911
Base Sequence
Chromosome Mapping
Cloning, Molecular
Comparative Study
DNA, Bacterial/genetics
Gene Expression Regulation, Bacterial
Genes, Bacterial
Genome, Bacterial
Molecular Sequence Data
Molecular Structure
Mycobacterium/*genetics/*metabolism/pathogenicity
Mycobacterium chelonae/genetics/metabolism/pathogenicity
Mycobacterium fortuitum/genetics/metabolism/pathogenicity
Mycobacterium phlei/genetics/metabolism/pathogenicity
Plasmids
Polymerase Chain Reaction
*Promoter Regions (Genetics)
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal/chemistry/metabolism
RNA, Ribosomal, 16S/genetics
Ribosomes/*metabolism
Sequence Alignment
Sequence Analysis, DNA
Support, Non-U.S. Gov't
Transcription, Genetic
Virulence/genetics
*rRNA Operon
|
| Remarks: |
One rRNA operon of all mycobacteria studied so far is located downstream from a gene thought to code for the enzyme UDP-N-acetylglucosamine carboxyvinyl transferase (UNAcGCT), which is important to cell wall synthesis. This operon has been designated rrnAf for fast-growing mycobacteria and rrnAs for slow growers. We have investigated the upstream sequences and promoter activities of rrnA operons of typical fast growers which also possess a second rrn (rrnBf) operon and of the rrnA operons of the fast growers Mycobacterium abscessus and Mycobacterium chelonae, which each have a single rrn operon per genome. These fast growers have a common strategy for increasing the efficiency of transcription of their rrnA operons, thereby increasing the cells' potential for ribosome synthesis. This strategy involves the use of multiple (three to five) promoters which may have arisen through successive duplication events. Thus we have identified a hypervariable multiple promoter region (HMPR) located between the UNAcGCT gene and the 16S rRNA coding region. Two promoters, P1 and PCL1, appear to play pivotal roles in mycobacterial rRNA synthesis; they are present in all of the species examined and are the only promoters used for rRNA synthesis by the pathogenic slow growers. P1 is located within the coding region of the UNAcGCT gene, and PCL1 has a characteristic sequence that is related to but distinct from that of the additional promoters. In fast-growing species, P1 and PCL1 produce less than 10% of rRNA transcripts, so the additional promoters found in the HMPR are important in increasing the potential for rRNA synthesis during rapid growth. In contrast, rrnB operons appear to be regulated by a single promoter; because less divergence has taken place, rrnB appears to be younger than rrnA. |
| URL: |
98037490 |
|
| 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 #: |
1300 |
| Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Approved Lists of Bacterial Names. |
| Volume: |
30 |
| Page(s): |
225-420 |
| Year: |
1980 |
|
| 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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