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Bacteria and Mycoplasmas detail

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Bacteria Collection: mycobacterium farcinogenes subsp. tchadense

NCTC Number: NCTC 10955
Current Name: mycobacterium farcinogenes subsp. tchadense
Original Strain Reference: 75
Other Collection No: ATCC 35753; CCM 6181; DSM 43637; 75
Previous Catalogue Name: Mycobacterium farcinogenes subsp. Tchadense
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: glucose agar,37, aerobic
Conditions for growth on liquid media: 7h9 broth,37, aerobic
Isolated From: mammal, bovine lymph node
16S rRNA Gene Sequence: >gb|Y11581|NCTC 10955|Mycobacterium farcinogenes 16S rRNA gene, partial.| gaacggaaaggccct... >gb|AF547921|DSM 43637|Mycobacterium farcinogenes strain DSM 43637 16S ribosomal RNA gene,partial sequence.| gtgcttaacacatgc... >gb|AF055333|ATCC35753|Mycobacterium farcinogenes 16S ribosomal RNA gene, partialsequence.| cgaacgctcgcggcg... >gb|AY457084|NCTC 10955T|Mycobacterium farcinogenes strain NCTC 10955T 16S ribosomal RNAgene, partial sequence.| tagagtttgatcctg...
23S rRNA Gene Sequence: >gb|U24517|ATCC 35753|Mycobacterium farcinogenes 23S rRNA, partial sequence.| tgcgcttacaatccg...
Bibliography: CHAMOISEAU G 1973 ANN MICROBIOL (INST PASTEUR) 124A 215
Extended Bibliography: showhide Show bibliography
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 #: 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 #: 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 #: 95455
Author(s): Devulder,G.;Perouse de Montclos,M.;Flandrois,J.P.
Journal: Int J Syst Evol Microbiol
Title: A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model
Volume: 55
Page(s): 293-302
Year: 2005
Keyword(s): Animals Bacterial Proteins/*genetics *Bacterial Typing Techniques Chaperonins/genetics DNA, Bacterial/analysis DNA-Directed RNA Polymerases/genetics Genes, rRNA Humans Mycobacterium/*classification/*genetics *Phylogeny Polymerase Chain Reaction RNA, Ribosomal, 16S/genetics *Sequence Analysis, DNA Superoxide Dismutase/genetics
Remarks: Advances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genus Mycobacterium cause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp), hsp65 (420 bp), rpoB (396 bp) and sod (408 bp) genes, were sequenced from 97 strains, including all available type strains of the genus Mycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification.
URL: 15653890
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 #: 2677
Author(s): Riddel,M.;Goodfellow,M.;Minnikin,D.E.;Minnikin,S.M.;Hutchinson,I.G.
Journal: J. Gen. Microbiol.
Title: Classification of Mycobacterium farcinogenes and Mycobacterium senegalense by immunodiffusion and thin-layer chromatography of long-chain components.
Volume: 128
Page(s): 1299-1307
Year: 1982
Ref #: 2678
Author(s): Riddel,M.;Goodfellow,M.
Journal: J. Gen. Microbiol.
Title: Numerical classification of Mycobacterium farcinogenes, Mycobacterium senegalense and related taxa.
Volume: 129
Page(s): 599-611
Year: 1983
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
Data: Type strain / P. Perreau, Maisons-Alfort, France in 1974 / G. Chamoiseau, Mauritiana / Bovine lymph node in 1963 / Chamoiseau, G. (1973) Ann. Microbiol. (Inst. Pasteur), 124 A, 215
Accession Date: 01/01/1974
History: ISOLATED BY CHAMOISEAU G MAURITIANA-PERREAU P MAISONS ALFORT PRE:FR
Authority: Chamoiseau 1973
Depositor: PERREAU P
Taxonomy: TaxLink: S1948 (Mycobacterium farcinogenes Chamoiseau 1973) - 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

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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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