Culture Collections

Bacteria and Mycoplasmas detail

Conditions of Supply of Microbial Pathogens: Safety





Bacteria Collection: Mycobacterium smegmatis

NCTC Number: NCTC 8159
Current Name: Mycobacterium smegmatis
Original Strain Reference: Cornell 3
Other Collection No: ATCC 19420; CORNELL 3; DSM 43756; JCM 5866; KCTC 9108
Previous Catalogue Name: Mycobacterium smegmatis
Type Strain: Yes
Family: Mycobacteriaceae
Hazard Group (ACDP): 2
Release Restrictions: Terms & Conditions of Supply of Microbial Pathogens: Safety
Conditions for growth on solid media: Columbia blood agar, 48-72 hours, 30°C, aerobic
Conditions for growth on liquid media: glucose broth,30, aerobic
Whole Genome Sequence: http://www.ebi.ac.uk/ena/data/view/ERS451418
Annotated Genome: ftp://ftp.sanger.ac.uk/pub/project/pathogens/NCTC3000/...
16S rRNA Gene Sequence: >gb|X76257|NCTC 8159|M.smegmatis (NCTC 8159) genes for 16S and 23s ribosomal RNA partial(381bp).| ctcctttctaaggag... >gb|X76256|NCTC 8159|M.smegmatis (NCTC 8159) gene for 16S ribosomal RNA partial (238bp).| gatcctcgctgccac... >gb|X76255|NCTC 8159|M.smegmatis (NCTC 8159) gene for 16S ribosomal RNA partial (207bp).| gggttgccccgaagc... >gb|AJ536041|TYPE STRAIN: DSM 43756|Mycobacterium smegmatis 16S rRNA gene.| gacgaacgctggcgg... >gb|AJ131761|ATCC 19420|Mycobacterium smegmatis 16S rRNA gene, strain ATCC 19420.| ggcggcgtgcttaac... >gb|AY457078|ATCC 19420|Mycobacterium smegmatis strain ATCC 19420 16S ribosomal RNA gene,partial sequence.| tagagtttgatcctg... >gb|AF059846|ATCC19420|Mycobacterium smegmatis strain ATCC19420 16S ribosomal RNA (rrs)gene, partial sequence.| agtcgaacggaaagg...
23S rRNA Gene Sequence: >gb|X76257|NCTC 8159|M.smegmatis (NCTC 8159) genes for 16S and 23s ribosomal RNA partial(381bp).| ctcctttctaaggag... >gb|X76258|NCTC 8159|M.smegmatis (NCTC 8159) genes for 23S and 5S ribosomal RNA partial(149bp).| caccccataacgttg... >gb|X76258|NCTC 8159|M.smegmatis (NCTC 8159) genes for 23S and 5S ribosomal RNA partial(149bp).| caccccataacgttg...
Extended Bibliography: showhide 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
Data: (ATCC 19420, JCM 5866) Type strain / R. E. Gordon, Plant Industry Station, Beltsville in 1950
Accession Date: 01/01/1950
History: GORDON R E, PLANT INDUSTRY STATION, BELTSVILLE, MARYLAND PRE:FR
Authority: (Trevisan 1889) Lehmann and Neumann 1899 (AL)
Depositor: GORDON R E
Taxonomy: TaxLink: S1980 (Mycobacterium smegmatis (Trevisan 1889) Lehmann and Neumann 1899) - Date of change: 5/02/2003
Biosafety Responsibility: It is the responsibility of the customer to ensure that their facilities comply with biosafety regulations for their own country

Additional Information

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The Culture Collections hold cell cultures, bacteria, fungi and virus strains from worldwide sources. Our scientists ensure that the identification of the cultures is correct and they remain unchanged from when they are first deposited with the Collection. Nevertheless, some of the data we provide about the cultures is supplied by the person depositing the strains and, although we have multiple checking procedures in place, we cannot always verify all their data. Please note that the Culture Collections cannot be held responsible for any inaccuracies in the data provided by the depositors.

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Available Formats

Ampoule (Bacteria)
Bacterial DNA - 2µg

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