| Extended Bibliography: |
Show bibliography
| Ref #: |
95444 |
| Author(s): |
Talaat,A.M.;Reimschuessel,R.;Trucksis,M. |
| Journal: |
Vet Microbiol |
| Title: |
Identification of mycobacteria infecting fish to the species level using polymerase chain reaction and restriction enzyme analysis |
| Volume: |
58 |
| Page(s): |
229-37 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/U92088
GENBANK/U92089
GENBANK/U92090
Animals
Base Sequence
Conserved Sequence
DNA Primers
Deoxyribonuclease BamHI
Deoxyribonucleases, Type II Site-Specific
*Fish Diseases
Fishes
Humans
Mycobacterium/*classification/genetics/*isolation & purification
Mycobacterium Infections/diagnosis/*veterinary
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
Restriction Mapping/*methods
|
| Remarks: |
An assay is described utilizing PCR technology for a rapid diagnostic test to identify fish infection with Mycobacterium marinum, M. fortuitum and M. chelonae. A 924 bp DNA fragment from a highly conserved area of the mycobacterial 16S rRNA gene was amplified using mycobacteria genus-specific primers and digested with restriction enzymes (BanI and ApaI). This examination yielded unique restriction patterns for each mycobacterial specie enabling identification of mycobacteria infecting fish to the species level. The protocol can be applied to purified DNA, a simple colony preparation or infected fish tissue. This protocol can be completed in 1-2 days. |
| URL: |
9453133 |
|
| 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 #: |
95504 |
| Author(s): |
Stinear,T.P.;Jenkin,G.A.;Johnson,P.D.;Davies,J.K. |
| Journal: |
J Bacteriol |
| Title: |
Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium marinum reveals evidence of recent divergence |
| Volume: |
182 |
| Page(s): |
6322-30 |
| Year: |
2000 |
| Keyword(s): |
GENBANK/AF271093
GENBANK/AF271094
GENBANK/AF271095
GENBANK/AF271097
Animals
Base Sequence
Electrophoresis, Gel, Pulsed-Field
*Genes, Bacterial
Humans
Molecular Sequence Data
Mycobacterium marinum/classification/*genetics
Mycobacterium ulcerans/classification/*genetics
Nucleic Acid Hybridization
Phylogeny
RNA, Bacterial/analysis
RNA, Ribosomal, 16S/analysis
Recombination, Genetic
Restriction Mapping
Sequence Alignment
Species Specificity
|
| Remarks: |
Previous studies of the 16S rRNA genes from Mycobacterium ulcerans and Mycobacterium marinum have suggested a very close genetic relationship between these species (99.6% identity). However, these organisms are phenotypically distinct and cause diseases with very different pathologies. To investigate this apparent paradox, we compared 3,306 nucleotides from the partial sequences of eight housekeeping and structural genes derived from 18 M. ulcerans strains and 22 M. marinum strains. This analysis confirmed the close genetic relationship inferred from the 16S rRNA data, with nucleotide sequence identity ranging from 98.1 to 99.7%. The multilocus sequence analysis also confirmed previous genotype studies of M. ulcerans that have identified distinct genotypes within a geographical region. Single isolates of both M. ulcerans and M. marinum that were shown by the sequence analysis to be the most closely related were then selected for further study. One- and two-dimensional pulsed-field gel electrophoresis was employed to compare the architecture and size of the genome from each species. Genome sizes of approximately 4.4 and 4.6 Mb were obtained for M. ulcerans and M. marinum, respectively. Significant macrorestriction fragment polymorphism was observed between the species. However, hybridization analysis of DNA cleaved with more frequently cutting enzymes identified significant preservation of the flanking sequence at seven of the eight loci sequenced. The exception was the 16S rRNA locus. Two high-copy-number insertion sequences, IS2404 and IS2606, have recently been reported in M. ulcerans, and significantly, these elements are not present in M. marinum. Hybridization of the AseI restriction fragments from M. ulcerans with IS2404 and IS2606 indicated widespread genome distribution for both of these repeated sequences. Taken together, these data strongly suggest that M. ulcerans has recently diverged from M. marinum by the acquisition and concomitant loss of DNA in a manner analogous to the emergence of M. tuberculosis, where species diversity is being driven mainly by the activity of mobile DNA elements. |
| URL: |
11053375 |
|
| 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 #: |
95489 |
| Author(s): |
Ucko,M.;Colorni,A.;Kvitt,H.;Diamant,A.;Zlotkin,A.;Knibb,W.R. |
| Journal: |
Appl Environ Microbiol |
| Title: |
Strain variation in Mycobacterium marinum fish isolates |
| Volume: |
68 |
| Page(s): |
5281-7 |
| Year: |
2002 |
| Keyword(s): |
Animals
*Bacterial Proteins
Chaperonins/*classification/genetics
DNA, Bacterial/analysis
Fishes/*microbiology
Mycobacterium marinum/*classification/genetics/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/*analysis/genetics
Restriction Mapping
Variation (Genetics)
|
| Remarks: |
A molecular characterization of two Mycobacterium marinum genes, 16S rRNA and hsp65, was carried out with a total of 21 isolates from various species of fish from both marine and freshwater environments of Israel, Europe, and the Far East. The nucleotide sequences of both genes revealed that all M. marinum isolates from fish in Israel belonged to two different strains, one infecting marine (cultured and wild) fish and the other infecting freshwater (cultured) fish. A restriction enzyme map based on the nucleotide sequences of both genes confirmed the divergence of the Israeli marine isolates from the freshwater isolates and differentiated the Israeli isolates from the foreign isolates, with the exception of one of three Greek isolates from marine fish which was identical to the Israeli marine isolates. The second isolate from Greece exhibited a single base alteration in the 16S rRNA sequence, whereas the third isolate was most likely a new Mycobacterium species. Isolates from Denmark and Thailand shared high sequence homology to complete identity with reference strain ATCC 927. Combined analysis of the two gene sequences increased the detection of intraspecific variations and was thus of importance in studying the taxonomy and epidemiology of this aquatic pathogen. Whether the Israeli M. marinum strain infecting marine fish is endemic to the Red Sea and found extremely susceptible hosts in the exotic species imported for aquaculture or rather was accidentally introduced with occasional imports of fingerlings from the Mediterranean Sea could not be determined. |
| URL: |
12406715 |
|
| 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 #: |
13165 |
| Author(s): |
Talaat,A.M.;Reimschuessel,R.;Trucksis,M. |
| Journal: |
Vet Microbiol |
| Title: |
Identification of mycobacteria infecting fish to the species level using polymerase chain reaction and restriction enzyme analysis |
| Volume: |
58 |
| Page(s): |
229-37 |
| Year: |
1998 |
| Keyword(s): |
GENBANK/U92088
GENBANK/U92089
GENBANK/U92090
Animal
Base Sequence
Conserved Sequence
DNA Primers
Deoxyribonuclease BamHI
Deoxyribonucleases, Type II Site-Specific
*Fish Diseases
Fishes
Human
Mycobacterium/*classification/genetics/*isolation & purification
Mycobacterium Infections/diagnosis/*veterinary
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
Restriction Mapping/*methods
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
|
| Remarks: |
An assay is described utilizing PCR technology for a rapid diagnostic test to identify fish infection with Mycobacterium marinum, M. fortuitum and M. chelonae. A 924 bp DNA fragment from a highly conserved area of the mycobacterial 16S rRNA gene was amplified using mycobacteria genus-specific primers and digested with restriction enzymes (BanI and ApaI). This examination yielded unique restriction patterns for each mycobacterial specie enabling identification of mycobacteria infecting fish to the species level. The protocol can be applied to purified DNA, a simple colony preparation or infected fish tissue. This protocol can be completed in 1-2 days. |
| URL: |
98115223 |
|
| Ref #: |
13195 |
| Author(s): |
Ucko,M.;Colorni,A.;Kvitt,H.;Diamant,A.;Zlotkin,A.;Knibb,W.R. |
| Journal: |
Appl Environ Microbiol |
| Title: |
Strain variation in Mycobacterium marinum fish isolates |
| Volume: |
68 |
| Page(s): |
5281-7 |
| Year: |
2002 |
| Keyword(s): |
Animal
Chaperonins/*classification/genetics
DNA, Bacterial/analysis
Fishes/*microbiology
Mycobacterium marinum/*classification/genetics/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/*analysis/genetics
Restriction Mapping
Support, Non-U.S. Gov't
Variation (Genetics)
|
| Remarks: |
A molecular characterization of two Mycobacterium marinum genes, 16S rRNA and hsp65, was carried out with a total of 21 isolates from various species of fish from both marine and freshwater environments of Israel, Europe, and the Far East. The nucleotide sequences of both genes revealed that all M. marinum isolates from fish in Israel belonged to two different strains, one infecting marine (cultured and wild) fish and the other infecting freshwater (cultured) fish. A restriction enzyme map based on the nucleotide sequences of both genes confirmed the divergence of the Israeli marine isolates from the freshwater isolates and differentiated the Israeli isolates from the foreign isolates, with the exception of one of three Greek isolates from marine fish which was identical to the Israeli marine isolates. The second isolate from Greece exhibited a single base alteration in the 16S rRNA sequence, whereas the third isolate was most likely a new Mycobacterium species. Isolates from Denmark and Thailand shared high sequence homology to complete identity with reference strain ATCC 927. Combined analysis of the two gene sequences increased the detection of intraspecific variations and was thus of importance in studying the taxonomy and epidemiology of this aquatic pathogen. Whether the Israeli M. marinum strain infecting marine fish is endemic to the Red Sea and found extremely susceptible hosts in the exotic species imported for aquaculture or rather was accidentally introduced with occasional imports of fingerlings from the Mediterranean Sea could not be determined. |
| URL: |
22293508 |
|
| 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 #: |
792 |
| Author(s): |
Aronson,J.D. |
| Journal: |
J. Infect. Dis. |
| Title: |
Spontaneous tuberculosis in salt water fish. |
| Volume: |
39 |
| Page(s): |
314-320 |
| Year: |
1926 |
|
| Ref #: |
13684 |
| Author(s): |
Stinear,T.P.;Jenkin,G.A.;Johnson,P.D.;Davies,J.K. |
| Journal: |
J Bacteriol |
| Title: |
Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium |
| Volume: |
182 |
| Page(s): |
6322-6330 |
| Year: |
2000 |
| Keyword(s): |
0 (RNA, Bacterial)
0 (RNA, Ribosomal, 16S)
Animal
Base Sequence
Comparative Study
Electrophoresis, Gel, Pulsed-Field
*Genes, Structural, Bacterial
Human
Molecular Sequence Data
Mycobacterium marinum/classification/*genetics
Mycobacterium ulcerans/classification/*genetics
Nucleic Acid Hybridization
Phylogeny
RNA, Bacterial/analysis
RNA, Ribosomal, 16S/analysis
Recombination, Genetic
Restriction Mapping
Sequence Alignment
Species Specificity
Support, Non-U.S. Gov't
|
| Remarks: |
Previous studies of the 16S rRNA genes from Mycobacterium ulcerans and |
| URL: |
20507800 |
|
|
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