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Bacteria and Mycoplasmas detail

Conditions of Supply of Microbial Pathogens: Safety





Bacteria Collection: Mycobacterium scrofulaceum

NCTC Number: NCTC 10803
Current Name: Mycobacterium scrofulaceum
Original Strain Reference: 1356
Other Collection No: ATCC 19981; DSM 43992; JCM 6381; L2238; PRISSICK 1356; TMC 1323
Previous Catalogue Name: Mycobacterium scrofulaceum
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: 7h10,37, aerobic
Conditions for growth on liquid media: nutrient broth,37, aerobic
Isolated From: human, cervical lymph node
16S rRNA Gene Sequence: >gb|AJ536034|TYPE STRAIN: DSM 43992|Mycobacterium scrofulaceum 16S rRNA gene.| gacgaacgctggcgg... >gb|AF480604|ATCC 19981|Mycobacterium scrofulaceum 16S ribosomal RNA gene, partialsequence.| gacgaacgctggcgg... >gb|AF059847|ATCC19981|Mycobacterium scrofulaceum strain ATCC19981 16S ribosomal RNA (rrs)gene, partial sequence.| agtcgaacggaaagg...
23S rRNA Gene Sequence: >gb|U24545|ATCC 19981|Mycobacterium scrofulaceum 23S rRNA, partial sequence.| tgtgcctacaatccg...
Bibliography: PRISSICK F H & MASSON A M 1957 CAN J MICROBIOL 3 91; PRISSICK F H & MASSON
Extended Bibliography: showhide Show bibliography
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 #: 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 #: 95496
Author(s): Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A.
Journal: J Clin Microbiol
Title: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species
Volume: 39
Page(s): 3637-48
Year: 2001
Keyword(s): *Databases, Nucleic Acid *Genes, rRNA Humans Internet Mycobacterium/*classification/genetics Mycobacterium Infections/*microbiology Phylogeny Quality Control RNA, Ribosomal, 16S/*genetics Reference Standards *Sequence Analysis, DNA Species Specificity
Remarks: The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.
URL: 11574585
Ref #: 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 #: 13151
Author(s): Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A.
Journal: J Clin Microbiol
Title: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species
Volume: 39
Page(s): 3637-48
Year: 2001
Keyword(s): *Databases, Nucleic Acid *Genes, rRNA Human Internet Mycobacterium/*classification/genetics Mycobacterium Infections/*microbiology Phylogeny Quality Control RNA, Ribosomal, 16S/*genetics Reference Standards *Sequence Analysis, DNA Species Specificity
Remarks: The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.
URL: 21458757
Ref #: 4493
Journal: Int. J. Syst. Bacteriol.
Volume: 19
Page(s): 260
Year: 1969
Ref #: 4494
Author(s): Prissick,F.H.;Masson,A.M.
Journal: Can. Med. Assoc. J.
Title: Cervical lymphadenitis in children caused by chromogenic mycobacteria.
Volume: 75
Page(s): 798-803
Year: 1956
Ref #: 4495
Author(s): Prissick,F.H.;Masson,A.M.
Journal: Can. J. Microbiol.
Title: Yellow-pigmented pathogenic mycobacteria from cervical lymphodenitis.
Volume: 3
Page(s): 91-100
Year: 1957
Ref #: 6924
Author(s): DeutschesInstitutfürNormungDIN.NormenausschußMedizin(NAMed)
Title: DIN 58959-7. Qualitätsmanagement in der medizinischen Mikrobiologie. Teil 7: Allgemeine Anforderungen an das Mitführen von Kontrollstämmen. Beiblatt 2: ATCC- und DSM-Nummern häufig verwendeter Kontrollstämme.
Year: 1997
Data: (Hauduroy L2238, ATCC 19981, TMC 1323) Type strain / ATCC in 1971 / P. Hauduroy / F. H. Prissick / Cervical lymph node / Prissick, F. H. & Masson, A. M. (1956) Can. med. Ass. J. 75, 798 / Prissick, F. H. & Masson, A. M. (1957) Can. J. Microbiol. 3, 91
Accession Date: 01/01/1971
History: HAUDUROY P-PRISSICK F H
Authority: Prissick and Masson 1956 (AL)
Depositor: ATCC
Taxonomy: TaxLink: S1976 (Mycobacterium scrofulaceum Prissick and Masson 1956) - 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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