| Extended Bibliography: |
Show bibliography
| Ref #: |
95532 |
| Author(s): |
Ji,Y.E.;Colston,M.J.;Cox,R.A. |
| Journal: |
Microbiology |
| Title: |
The ribosomal RNA (rrn) operons of fast-growing mycobacteria: primary and secondary structures and their relation to rrn operons of pathogenic slow-growers |
| Volume: |
140 ( Pt 10) |
| Page(s): |
2829-40 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X76255
GENBANK/X76256
GENBANK/X76257
GENBANK/X76258
Base Sequence
DNA Probes
Molecular Conformation
Molecular Sequence Data
Molecular Structure
Mycobacterium/*genetics/metabolism
Polymerase Chain Reaction
RNA, Ribosomal, 16S/chemistry/*genetics
RNA, Ribosomal, 23S/chemistry/*genetics
Sequence Homology
*rRNA Operon
|
| Remarks: |
The two ribosomal RNA (rrn) operons (rrnA and rrnB) of Mycobacterium smegmatis were investigated. The leader regions, part of the 16S rRNA genes, the spacer-1 regions, part of the 23S rRNA genes, and the spacer-2 regions were amplified by PCR or by inverse PCR and the products were cloned and sequenced. No differences in the sequences of the two operons were detected downstream from the Box A antitermination element of the leader region. Upstream from Box A a slow-grower-like Box B antitermination element was found in rrnA but not in rrnB. Primer extension experiments revealed that the start of transcription lies at least 370 nucleotides upstream from the 5'-end of the 16S rRNA gene and an RNase processing site near to the Box A element. Secondary structures were deduced for pre-16S rRNA and pre-23S rRNA which are distinct from, but closely related to, the corresponding structures of slow-growing mycobacteria. On the basis of these results it is proposed that the emergence of the slow-growers from the main mycobacterial line was coincident with the deletion of a segment of DNA spanning an rrnB-like operon, leaving an rrnA-like operon as the sole source of rRNA. An explanation is also proposed for the need for two Box A motifs in the transcription of an rrn operon based on competition between the polymerase and the nascent 30S subunit for either protein S10 and/or Box A sequences. |
| URL: |
8000546 |
|
| 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 #: |
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 #: |
60358 |
| Author(s): |
Brown,B.A.;Springer,B.;Steingrube,V.A.;Wilson,R.W.;Pfyffer,G.E.;Garcia,M.J.;Menendez,M.C.;Rodriguez-Salgado,B.;Jost KC,J.r.;Chiu,S.H.;Onyi,G.O.;Bottger,E.C.;Wallace RJ,J.r. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Mycobacterium wolinskyi sp. nov. and Mycobacterium goodii sp. nov., two new rapidly growing species related to Mycobacterium smegmatis and associated with human wound infections: a cooperative study from the International Working Group on Mycobacterial Taxonomy |
| Volume: |
49 Pt 4 |
| Page(s): |
1493-511 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AJ011335
GENBANK/AJ131761
GENBANK/Y12871
GENBANK/Y12872
GENBANK/Y12873
Adolescent
Adult
Aged
Aged, 80 and over
*Bacterial Proteins
Bacterial Typing Techniques
Base Composition
Base Sequence
Chaperonins/genetics
Chromatography, High Pressure Liquid
DNA, Bacterial/chemistry/genetics
Female
Genes, rRNA/genetics
Humans
Male
Microbial Sensitivity Tests
Middle Aged
Molecular Sequence Data
Mycobacterium/*classification/genetics/isolation & purification/physiology
Mycobacterium Infections/*microbiology
Mycobacterium smegmatis/classification/genetics/isolation & purification
Nucleic Acid Hybridization
Polymerase Chain Reaction
Polymorphism, Restriction Fragment Length
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Wound Infection/*microbiology
|
| Remarks: |
Previous investigations demonstrated three taxonomic groups among 22 clinical isolates of Mycobacterium smegmatis. These studies were expanded to 71 clinical isolates, of which 35 (49%) (group 1) were identical to five ATCC reference strains including the type strain ATCC 19420T. Twenty-eight isolates (39%) were group 2, and eight isolates (11%) were group 3. Isolates of groups 2 and 3 were most often associated with post-traumatic or post-surgical wound infections including osteomyelitis, were susceptible to sulfamethoxazole, amikacin, imipenem and the tetracyclines, variably resistant to clarithromycin, and susceptible (group 1), intermediately resistant (group 2) or resistant (group 3) to tobramycin. The three groups were similar by routine biochemical and growth characteristics, but had different mycolic acid dimethoxy-4-coumarinylmethyl ester elution patterns by HPLC and different PCR-restriction enzyme patterns of a 439 bp fragment of the hsp-65 gene. Group 3 isolates differed from group 1 by 18 bp by 16S rRNA sequencing and exhibited < 25% homology by DNA-DNA hybridization, being most closely related to Mycobacterium mageritense. The 16S rRNA of group 1 and group 2 isolates differed by only 3 bp, but by DNA-DNA hybridization they exhibited only 40% homology. The following names are proposed: Mycobacterium goodii sp. nov. for group 2 isolates (type strain ATCC 700504T = MO69T), Mycobacterium wolinskyi sp. nov. for group 3 isolates (type strain ATCC 700010T = MO739T) and Mycobacterium smegmatis sensu stricto for group 1 isolates. |
| URL: |
10555330 |
|
| 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 #: |
59868 |
| Author(s): |
Adekambi,T.;Colson,P.;Drancourt,M. |
| Journal: |
J Clin Microbiol |
| Title: |
rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria |
| Volume: |
41 |
| Page(s): |
5699-708 |
| Year: |
2003 |
| Keyword(s): |
Base Sequence
Biological Markers/analysis
DNA Primers
DNA-Directed RNA Polymerases/*analysis/genetics
Databases, Nucleic Acid
Mycobacterium/*classification/enzymology/*growth & development/isolation &
purification
Phylogeny
Polymerase Chain Reaction
Sequence Homology, Nucleic Acid
|
| Remarks: |
Nonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) are increasingly isolated in clinical microbiology laboratories. Their accurate identification remains problematic because classification is labor intensive work and because new taxa are not often incorporated into classification databases. Also, 16S rRNA gene sequence analysis underestimates RGM diversity and does not distinguish between all taxa. We determined the complete nucleotide sequence of the rpoB gene, which encodes the bacterial beta subunit of the RNA polymerase, for 20 RGM type strains. After using in-house software which analyzes and graphically represents variability stretches of 60 bp along the nucleotide sequence, our analysis focused on a 723-bp variable region exhibiting 83.9 to 97% interspecies similarity and 0 to 1.7% intraspecific divergence. Primer pair Myco-F-Myco-R was designed as a tool for both PCR amplification and sequencing of this region for molecular identification of RGM. This tool was used for identification of 63 RGM clinical isolates previously identified at the species level on the basis of phenotypic characteristics and by 16S rRNA gene sequence analysis. Of 63 clinical isolates, 59 (94%) exhibited <2% partial rpoB gene sequence divergence from 1 of 20 species under study and were regarded as correctly identified at the species level. Mycobacterium abscessus and Mycobacterium mucogenicum isolates were clearly distinguished from Mycobacterium chelonae; Mycobacterium mageritense isolates were clearly distinguished from "Mycobacterium houstonense." Four isolates were not identified at the species level because they exhibited >3% partial rpoB gene sequence divergence from the corresponding type strain; they belonged to three taxa related to M. mucogenicum, Mycobacterium smegmatis, and Mycobacterium porcinum. For M. abscessus and M. mucogenicum, this partial sequence yielded a high genetic heterogeneity within the clinical isolates. We conclude that molecular identification by analysis of the 723-bp rpoB sequence is a rapid and accurate tool for identification of RGM. |
| URL: |
14662964 |
|
| Ref #: |
59859 |
| Author(s): |
Adekambi,T.;Drancourt,M. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing |
| Volume: |
54 |
| Page(s): |
2095-105 |
| Year: |
2004 |
| Keyword(s): |
GENBANK/AL450380
GENBANK/AY147163
GENBANK/AY147164
GENBANK/AY147165
GENBANK/AY147166
GENBANK/AY147167
GENBANK/AY147169
GENBANK/AY147170
GENBANK/AY147171
GENBANK/AY147172
GENBANK/AY147173
GENBANK/AY147174
GENBANK/AY262735
GENBANK/AY262736
GENBANK/AY262737
GENBANK/AY262738
GENBANK/AY262739
GENBANK/AY262740
GENBANK/AY262742
GENBANK/AY262743
GENBANK/AY457066
GENBANK/AY457067
GENBANK/AY457068
GENBANK/AY457069
GENBANK/AY457070
GENBANK/AY457071
GENBANK/AY457072
GENBANK/AY457073
GENBANK/AY457074
GENBANK/AY457075
GENBANK/AY457076
GENBANK/AY457077
GENBANK/AY457078
GENBANK/AY457079
GENBANK/AY457080
GENBANK/AY457081
GENBANK/AY457082
GENBANK/AY457083
GENBANK/AY457084
GENBANK/AY458064
GENBANK/AY458065
GENBANK/AY458066
GENBANK/AY458067
GENBANK/AY458068
GENBANK/AY458069
GENBANK/AY458070
GENBANK/AY458071
GENBANK/AY458072
GENBANK/AY458073
GENBANK/AY458074
GENBANK/AY458075
GENBANK/AY458076
GENBANK/AY458077
GENBANK/AY458078
GENBANK/AY458079
GENBANK/AY458080
GENBANK/AY458081
GENBANK/AY458083
GENBANK/AY458084
GENBANK/AY458085
GENBANK/AY458086
GENBANK/AY458087
GENBANK/AY458088
GENBANK/AY458089
GENBANK/AY458090
GENBANK/AY458091
GENBANK/AY458092
GENBANK/AY458093
GENBANK/AY458094
GENBANK/AY458095
GENBANK/AY458096
GENBANK/AY458097
GENBANK/AY458098
GENBANK/AY458099
GENBANK/AY458100
GENBANK/AY458101
GENBANK/AY458102
GENBANK/AY458103
GENBANK/AY458104
GENBANK/AY458105
GENBANK/AY458106
GENBANK/AY458107
GENBANK/AY458108
GENBANK/AY458109
GENBANK/AY458110
GENBANK/AY458111
GENBANK/AY458112
GENBANK/AY458113
GENBANK/AY458114
GENBANK/AY458115
GENBANK/AY458116
GENBANK/AY458117
GENBANK/AY458118
GENBANK/AY458119
GENBANK/AY458120
Bacterial Proteins/*genetics
Chaperonins/*genetics
DNA, Bacterial/chemistry/isolation & purification
DNA, Ribosomal/chemistry/isolation & purification
DNA-Directed RNA Polymerases/*genetics
Genes, rRNA
Molecular Sequence Data
Mycobacteria, Atypical/classification/*genetics
Mycobacterium/classification/*genetics
Mycobacterium chelonae/classification/genetics
Mycobacterium fortuitum/classification/genetics
Mycobacterium smegmatis/classification/genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Rec A Recombinases/*genetics
Sequence Analysis, DNA
Superoxide Dismutase/*genetics
|
| Remarks: |
The current classification of non-pigmented and late-pigmenting rapidly growing mycobacteria (RGM) capable of producing disease in humans and animals consists primarily of three groups, the Mycobacterium fortuitum group, the Mycobacterium chelonae-abscessus group and the Mycobacterium smegmatis group. Since 1995, eight emerging species have been tentatively assigned to these groups on the basis of their phenotypic characters and 16S rRNA gene sequence, resulting in confusing taxonomy. In order to assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene (1483-1489 bp), rpoB (3486-3495 bp) and recA (1041-1056 bp) and partial sequences of hsp65 (420 bp) and sodA (441 bp) were determined in 19 species of RGM. Phylogenetic trees based upon each gene sequence, those based on the combined dataset of the five gene sequences and one based on the combined dataset of the rpoB and recA gene sequences were then compared using the neighbour-joining, maximum-parsimony and maximum-likelihood methods after using the incongruence length difference test. Combined datasets of the five gene sequences comprising nearly 7000 bp and of the rpoB+recA gene sequences comprising nearly 4600 bp distinguished six phylogenetic groups, the M. chelonae-abscessus group, the Mycobacterium mucogenicum group, the M. fortuitum group, the Mycobacterium mageritense group, the Mycobacterium wolinskyi group and the M. smegmatis group, respectively comprising four, three, eight, one, one and two species. The two protein-encoding genes rpoB and recA improved meaningfully the bootstrap values at the nodes of the different groups. The species M. mucogenicum, M. mageritense and M. wolinskyi formed new groups separated from the M. chelonae-abscessus, M. fortuitum and M. smegmatis groups, respectively. The M. mucogenicum group was well delineated, in contrast to the M. mageritense and M. wolinskyi groups. For phylogenetic organizations derived from the hsp65 and sodA gene sequences, the bootstrap values at the nodes of a few clusters were <70 %. In contrast, phylogenetic organizations obtained from the 16S rRNA, rpoB and recA genes were globally similar to that inferred from combined datasets, indicating that the rpoB and recA genes appeared to be useful tools in addition to the 16S rRNA gene for the investigation of evolutionary relationships among RGM species. Moreover, rpoB gene sequence analysis yielded bootstrap values higher than those observed with recA and 16S rRNA genes. Also, molecular signatures in the rpoB and 16S rRNA genes of the M. mucogenicum group showed that it was a sister group of the M. chelonae-abscessus group. In this group, M. mucogenicum ATCC 49650(T) was clearly distinguished from M. mucogenicum ATCC 49649 with regard to analysis of the five gene sequences. This was in agreement with phenotypic and biochemical characteristics and suggested that these strains are representatives of two closely related, albeit distinct species. |
| URL: |
15545441 |
|
| Ref #: |
13176 |
| Author(s): |
Brown,B.A.;Springer,B.;Steingrube,V.A.;Wilson,R.W.;Pfyffer,G.E.;Garcia,M.J.;Menendez,M.C.;Rodriguez-Salgado,B.;Jost KC,J.r.;Chiu,S.H.;Onyi,G.O.;Bottger,E.C.;Wallace RJ,J.r. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Mycobacterium wolinskyi sp. nov. and Mycobacterium goodii sp. nov., two new rapidly growing species related to Mycobacterium smegmatis and associated with human wound infections: a cooperative study from the International Working Group on Mycobacterial Taxonomy |
| Volume: |
49 Pt 4 |
| Page(s): |
1493-511 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AJ011335
GENBANK/AJ131761
GENBANK/Y12871
GENBANK/Y12872
GENBANK/Y12873
Adolescent
Adult
Aged
Aged, 80 and over
Bacterial Typing Techniques
Base Composition
Base Sequence
Chaperonins/genetics
Chromatography, High Pressure Liquid
DNA, Bacterial/chemistry/genetics
Female
Genes, rRNA/genetics
Human
Male
Microbial Sensitivity Tests
Middle Age
Molecular Sequence Data
Mycobacterium/*classification/genetics/isolation & purification/physiology
Mycobacterium Infections/*microbiology
Mycobacterium smegmatis/classification/genetics/isolation & purification
Nucleic Acid Hybridization
Polymerase Chain Reaction
Polymorphism, Restriction Fragment Length
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Wound Infection/*microbiology
|
| Remarks: |
Previous investigations demonstrated three taxonomic groups among 22 clinical isolates of Mycobacterium smegmatis. These studies were expanded to 71 clinical isolates, of which 35 (49%) (group 1) were identical to five ATCC reference strains including the type strain ATCC 19420T. Twenty-eight isolates (39%) were group 2, and eight isolates (11%) were group 3. Isolates of groups 2 and 3 were most often associated with post-traumatic or post-surgical wound infections including osteomyelitis, were susceptible to sulfamethoxazole, amikacin, imipenem and the tetracyclines, variably resistant to clarithromycin, and susceptible (group 1), intermediately resistant (group 2) or resistant (group 3) to tobramycin. The three groups were similar by routine biochemical and growth characteristics, but had different mycolic acid dimethoxy-4-coumarinylmethyl ester elution patterns by HPLC and different PCR-restriction enzyme patterns of a 439 bp fragment of the hsp-65 gene. Group 3 isolates differed from group 1 by 18 bp by 16S rRNA sequencing and exhibited < 25% homology by DNA-DNA hybridization, being most closely related to Mycobacterium mageritense. The 16S rRNA of group 1 and group 2 isolates differed by only 3 bp, but by DNA-DNA hybridization they exhibited only 40% homology. The following names are proposed: Mycobacterium goodii sp. nov. for group 2 isolates (type strain ATCC 700504T = MO69T), Mycobacterium wolinskyi sp. nov. for group 3 isolates (type strain ATCC 700010T = MO739T) and Mycobacterium smegmatis sensu stricto for group 1 isolates. |
| URL: |
20023030 |
|
| Ref #: |
13682 |
| 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 |
| Volume: |
40 |
| Page(s): |
707-711 |
| Year: |
2002 |
| Keyword(s): |
0 (DNA, Ribosomal Spacer)
0 (RNA, Ribosomal, 16S)
0 (RNA, Ribosomal, 23S)
Animal
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
Support, Non-U.S. Gov't
|
| Remarks: |
16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA |
| URL: |
21683667 |
|
| 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 #: |
750 |
| Author(s): |
Gordon,R.E.;Mihm,J.M. |
| Journal: |
J. Gen. Microbiol. |
| Title: |
A comparison of four species of mycobacteria. |
| Volume: |
21 |
| Page(s): |
736-748 |
| Year: |
1959 |
|
| Ref #: |
13691 |
| Author(s): |
Ji,Y.E.;Colston,M.J.;Cox,R.A. |
| Journal: |
Microbiology |
| Title: |
The ribosomal RNA (rrn) operons of fast-growing mycobacteria: primary and |
| Volume: |
140 ( Pt 10) |
| Page(s): |
2829-2840 |
| Year: |
1994 |
| Keyword(s): |
0 (DNA Probes)
0 (RNA, Ribosomal, 16S)
0 (RNA, Ribosomal, 23S)
Base Sequence
DNA Probes
Molecular Conformation
Molecular Sequence Data
Molecular Structure
Mycobacterium/*genetics/metabolism
Polymerase Chain Reaction
RNA, Ribosomal, 16S/chemistry/*genetics
RNA, Ribosomal, 23S/chemistry/*genetics
Sequence Homology
Support, Non-U.S. Gov't
*rRNA Operon
|
| Remarks: |
The two ribosomal RNA (rrn) operons (rrnA and rrnB) of Mycobacterium |
| URL: |
95093625 |
|
|
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