New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region

Microbiology (United Kingdom) - Tập 142 Số 1 - Trang 3-16 - 1996
Volker Gürtler1, Vilma A. Stanisich2
1Department of Microbiology, Austin and Repatriation Medical Centre (Repatriation Campus), Heidelberg West 3081, Victoria, Australia.
2School of Microbiology, La Trobe University, Bundoora, 3083, Victoria, Australia

Tóm tắt

Từ khóa


Tài liệu tham khảo

Abed, 1995a, Demonstration of Mycobacterium kansasii species heterogeneity by the amplification of the 16S–23S spacer region, J Med Microbiol, A3, 156, 10.1099/00222615-43-2-156

Abed, 1995b, Efficient discrimination of Mycobacterium tuberculosis strains by 16S–23S spacer region-based random amplified polymorphic DNA analysis, J Clin Microbiol, 33, 1418, 10.1128/JCM.33.5.1418-1420.1995

Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol Rev, 59, 143, 10.1128/MR.59.1.143-169.1995

Amikam, 1984, Mycoplasmas (Mollicutes) have a low number of rRNA genes, J Bacteriol, 158, 376, 10.1128/JB.158.1.376-378.1984

Andresson, 1994, The sequence of the single 16S rRNA gene of the thermophilic eubacterium Rhodo-thermus marinus reveals a distant relationship to the group containing Flexibacter, Bacteroides, and Cytophaga species, J Bacteriol, 176, 6165, 10.1128/JB.176.20.6165-6169.1994

Auriol, 1995, Characterization of serogroup A Neisseria meningitidis strains by rRNA gene restriction patterns and PCR: correlation with the results of serotyping, subtyping and multilocus enzyme electrophoresis, FEMS Immunol Med Microbiol, 10, 219, 10.1111/j.1574-695X.1995.tb00036.x

Bacot, 1991, Novel tRNA gene organization in the 16S–23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster, J Bacteriol, 173, 4234, 10.1128/JB.173.13.4234-4236.1991

Barry, 1991, The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria PCR, Methods Appl, 1, 51

Bercovier, 1986, Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome, Biochem Biophys Res Commun, 136, 1136, 10.1016/0006-291X(86)90452-3

Bourque, 1995, Comparative analyisis of the 16S to 23S intergenic spacer sequences of Bacillus thuringiensis strains and subspecies and of closely related species, Appl Environ Microbiol, 61, 1623, 10.1128/AEM.61.4.1623-1626.1995

Brosius, 1980, Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli, Proc Natl Acad Sci USA, 77, 201, 10.1073/pnas.77.1.201

Brosius, 1981, Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli, J Mol Biol, 148, 107, 10.1016/0022-2836(81)90508-8

Campbell, 1993, Studies on the large subunit ribosomal RNA genes and intergenic spacer regions of non-proteolytic Clostridium botulinum types B, E and F, Res Microbiol, 144, 171, 10.1016/0923-2508(93)90042-Z

Cartwright, 1995, PCR amplification of rRNA intergenic spacer regions as a method for epidemiologic typing of Clostridium difficile, J Clin Microbiol, 33, 184, 10.1128/JCM.33.1.184-187.1995

Dasen, 1994, Characterization of PCR-ribotyping for Burkhoideria (Pseudomonas) cepacia, J Clin Microbiol, 32, 2422, 10.1128/JCM.32.10.2422-2424.1994

Dolzani, 1994, Typing of Staphylococcus aureus by amplification of the 16S–23S rRNA intergenic spacer sequences, FEMS Microbiol Lett, 119, 167

Dolzani, 1995, Identification of Acinetobacter isolates in the A. calcoaceticus-A. baumannii complex by restriction analysis of the 16S–23S rRNA intergenic spacer sequences, J Clin Microbiol, 33, 1108, 10.1128/JCM.33.5.1108-1113.1995

Dryden, 1990, Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides, Nucleic Acids Res, 18, 7267, 10.1093/nar/18.24.7267

East, 1993, Molecular characterization of DNA encoding 23S rRNA and 16S–23S rRNA intergenic spacer regions of Aeromonas hydrophila, FEMS Microbiol Lett, 106, 129

East, 1992, Analysis of DNA encoding 23S rRNA and 16S–23S rRNA intergenic spacer regions from Plesiomonas shigelloides, FEMS Microbiol Lett, 74, 57

Emond, 1993, A ribosomal DNA fragment of Listeria monocytogenes and its use as a genus specific probe in an aqueous-phase hybridization assay, Appl Environ Microbiol, 59, 2690, 10.1128/AEM.59.8.2690-2697.1993

Feingold, 1985, Organization and nucleotide sequence analysis of an rRNA and tRNA gene cluster from Caulobacter crescentus, J Bacteriol, 163, 155, 10.1128/JB.163.1.155-166.1985

Fleischmann, 1995, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, 269, 496, 10.1126/science.7542800

Frothingham, 1993, Sequence-based differentiation of strains in the Mycobacterium avium complex, J Bacteriol, 175, 2818, 10.1128/JB.175.10.2818-2825.1993

Frothingham, 1994, Molecular phylogeny of the Mycobacterium avium complex demonstrates clinically meaningful divisions, J Infect Dis, 169, 305, 10.1093/infdis/169.2.305

Gamier, 1991, Cloning, mapping, and molecular characterization of the rRNA operons of Clostridium perfringens, J Bacteriol, 173, 5431, 10.1128/JB.173.17.5431-5438.1991

van der Giessen, 1994, Comparison of the 23S ribosomal RNA genes and the spacer region between the 16S and 23S rRNA genes of the closely related Mycobacterium avium and Mycobacterium paratuberculosis and the fast-growing Mycobacterium phlei, Microbiology, 140, 1103, 10.1099/13500872-140-5-1103

Gill, 1994, Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates, Can J Microbiol, 40, 541, 10.1139/m94-087

Glennon, 1994, The ribosomal intergenic spacer region: a target for the PCR based diagnosis of tuberculosis, Tubercle Lung Dis, 75, 353, 10.1016/0962-8479(94)90081-7

Green, 1985, Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB, Gene, 37, 261, 10.1016/0378-1119(85)90281-1

Griffen, 1992, Strain identification of Actinobacillus actinomycetemcomitans using the polymerase chain reaction, Oral Microbiol Immunol, 7, 240, 10.1111/j.1399-302X.1992.tb00032.x

Gürtler, 1993, Typing of Clostridium difficile strains by PCR-amplification of variable length 16S–23S rDNA spacer regions, J Gen Microbiol, 139, 3089, 10.1099/00221287-139-12-3089

Gürtler, 1995, Typing of Staphylococcus aureus strains by PCR-amplification of variable length 16S–23S rDNA spacer regions: characterization of spacer sequences, Microbiology, 141, 1255, 10.1099/13500872-141-5-1255

Hall, 1994, Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria?, Microbiology, 140, 197, 10.1099/13500872-140-1-197

Harasawa, 1993, Detection and tentative identification of dominant mycoplasma species in cell cultures by restriction analysis of the 16S–23S rRNA intergenic spacer regions, Res Microbiol, 144, 489, 10.1016/0923-2508(93)90057-9

Harvey, 1988, Loss of the spacer loop sequence from the rrnB operon in the Escherichia coli K-12 subline that bears the relA1 mutation, J Bacteriol, 170, 1235, 10.1128/JB.170.3.1235-1238.1988

Hookey, 1995, Intergenic 16S rRNA gene (rDNA)-23S rDNA sequence length polymorphisms in members of the family Legionellaceae, J Clin Microbiol, 33, 2377, 10.1128/JCM.33.9.2377-2381.1995

Iwami, 1984, Nucleotide sequence of the rrnB 16S ribosomal RNA gene from Mycoplasma capricolum, Mol & Gen Genet, 196, 317, 10.1007/BF00328065

Jannes, 1993, Polyphasic taxonomy leading to the proposal of Moraxella canis sp. nov. for Moraxella catarrhalis-like strains, Int J Syst Bacteriol, 43, 438, 10.1099/00207713-43-3-438

Jarsch, 1983, DNA sequence of the 16S rRNA/23S rRNA intercistronic spacer of two rDNA operons of the archae-bacterium Methanococcus vannielii, Nucleic Acids Res, 11, 7537, 10.1093/nar/11.21.7537

Jensen, 1993, Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions, PCR Methods Appl, 3, 186, 10.1101/gr.3.3.186

Jensen, 1993, Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms, Appl Environ Microbiol, 59, 945, 10.1128/AEM.59.4.945-952.1993

Kim, 1993, Gene organization and primary structure of a ribosomal RNA gene cluster from Streptomyces griseus subsp. griseus, Gene, 132, 21, 10.1016/0378-1119(93)90510-A

Kjems, 1987, Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archae-bacterium Thermoproteus tenax, Nucleic Acids Res, 15, 4821, 10.1093/nar/15.12.4821

Kostman, 1992, Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping, J Clin Microbiol, 30, 2084, 10.1128/JCM.30.8.2084-2087.1992

Kostman, 1995, A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping, J Infect Dis, 171, 204, 10.1093/infdis/171.1.204

Kuske, 1992, Phylogenetic relationships between the western aster yellows mycoplasmalike organism and other prokaryotes established by 16S rRNA gene sequence, Int J Syst Bacteriol, 42, 226, 10.1099/00207713-42-2-226

Lane, 1985, Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc Natl Acad Sci USA, 82, 6955, 10.1073/pnas.82.20.6955

Leys, 1994, Detection and strain identification of Actinobacillus actinomycetemcomitans by nested PCR, J Clin Microbiol, 32, 1288, 10.1128/JCM.32.5.1288-1294.1994

Liveris, 1995, Molecular typing of Borrelia burgdorferi sensu lato by PCR-restriction fragment length polymorphism analysis, J Clin Microbiol, 33, 589, 10.1128/JCM.33.3.589-595.1995

Loughney, 1982, tRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis, Nucleic Acids Res, 10, 1607, 10.1093/nar/10.5.1607

Ludwig, 1992, Complete 23 S ribosomal RNA sequences of gram-positive bacteria with a low DNA G + C content, Syst Appl Microbiol, 15, 487, 10.1016/S0723-2020(11)80107-4

McLaughlin, 1993, Amplification of rDNA loci to detect and type Neisseria meningitidis and other eubacteria, Mol Cell Probes, 7, 7, 10.1006/mcpr.1993.1002

Maddison, 1992, MacClade: Analysis of Phytogeny and Character Evolution. Version 3.0

Marconi, 1995, Identification of novel insertion elements, restriction fragment length polymorphism patterns, and discontinuous 23S rRNA in lyme disease spirochetes: phylogenetic analyses of rRNA genes and their intergenic spacers in Borrelia japonica sp. nov. and genomic group 21038 (Borrelia andersonii sp. nov.) isolates, J Clin Microbiol, 33, 2427, 10.1128/JCM.33.9.2427-2434.1995

Martirosian, 1995, PCR ribotyping and arbitrarily primed PCR for typing strains of Clostridium difficile from a Polish maternity hospital, J Clin Microbiol, 33, 2016, 10.1128/JCM.33.8.2016-2021.1995

Matar, 1993, Polymerase chain reaction-based restriction fragment length polymorphism analysis of a fragment of the ribosomal operon from Rochalimaea species for subtyping, J Clin Microbiol, 31, 1730, 10.1128/JCM.31.7.1730-1734.1993

Minnick, 1994, Characterization of the 16S–23S rRNA intergenic spacer of Bartonella bacilliformis, Gene, 143, 149, 10.1016/0378-1119(94)90622-X

Morgan, 1977, Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli, Proc Natl Acad Sci USA, 74, 2710, 10.1073/pnas.74.7.2710

Mullis, 1987, Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction, Methods Enzymol, 155, 335, 10.1016/0076-6879(87)55023-6

Nakagawa, 1992, Acholeplasma laidlawii has tRNA genes in the 16S–23S spacer of the rRNA operon, J Bacteriol, 174, 8163, 10.1128/JB.174.24.8163-8165.1992

Nakagawa, 1994, Detection of alcohol-tolerant hiochi bacteria by PCR, Appl Environ Microbiol, 60, 637, 10.1128/AEM.60.2.637-640.1994

Nastasi, 1995, Epidemiological evaluation by PCR ribotyping of sporadic and outbreak-associated strains of Salmonella enterica serotype Typhimurium, Res Microbiol, 146, 99, 10.1016/0923-2508(96)80274-9

Navarro, 1992, Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer, Arch Microbiol, 151, 107, 10.1007/BF00245277

Neefs, 1990, Compilation of small ribosomal subunit RNA sequences, Nucleic Acids Res, 18, 2237, 10.1093/nar/18.suppl.2237

Normand, 1992, Analysis of a ribosomal RNA operon in the actinomycete Frankia, Gene, 111, 119, 10.1016/0378-1119(92)90612-S

Nour, 1994, Genotypic and phenotypic diversity of Rhizobium isolated from chickpea (Cicer arietinum L.), Can J Microbiol, 40, 345, 10.1139/m94-057

Nowak, 1995, PCR differentiation of seventeen genospecies of Acinetobacter, FEMS Microbiol Lett, 126, 181, 10.1111/j.1574-6968.1995.tb07414.x

Olsen, 1985, Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications, J Mol Evol, 22, 301, 10.1007/BF02115685

Olsen, 1991, The ribosomal RNA database project, Nucleic Acids Res, 19, 2017, 10.1093/nar/19.suppl.2017

Pernodet, 1989, Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens, Gene, 79, 33, 10.1016/0378-1119(89)90090-5

Ponsonnet, 1994, Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions, Arch Microbiol, 161, 300

Rossau, 1992, DNA probes for Bordetella species and a colorimetric reverse hybridization assay for the detection of Bordetella pertussis, Mol Cell Probes, 6, 281, 10.1016/0890-8508(92)90003-G

Roux, 1995a, Inter- and intraspecies identification of Bartonella (Rochalimaea) species, J Clin Microbiol, 33, 1573, 10.1128/JCM.33.6.1573-1579.1995

Roux, 1995b, The 16S–23S rRNA intergenic spacer region of Bartonella (Rochalimaea) species is longer than usually described in other bacteria, Gene, 156, 107, 10.1016/0378-1119(94)00919-J

Sagredo, 1992, Organization of the 16S–23S intergenic spacer region of the two rRNA operons from Thiobacillus ferooxidans, Geomicrobiol J, 10, 239, 10.1080/01490459209377924

Salzano, 1994, Genotyping of Streptococcus thermophilus evidenced by restriction analysis of ribosomal DNA, Res Microbiol, 145, 651, 10.1016/0923-2508(94)90036-1

Sawada, 1984, Organization of ribosomal RNA genes in Mycoplasma capricolum, Mol & Gen Genet, 196, 311, 10.1007/BF00328064

Sechi, 1993, Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC 9790, J Bacteriol, 175, 3213, 10.1128/JB.175.10.3213-3219.1993

Sheffield, 1989, Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes, Proc Natl Acad Sci USA, 86, 232, 10.1073/pnas.86.1.232

Smith-Vaughan, 1995, Long PCR-ribotyping of nontypable Haemophilus influenzae, J Clin Microbiol, 33, 1192, 10.1128/JCM.33.5.1192-1195.1995

Suzuki, 1988, Molecular cloning and characterization of an rRNA operon in Streptomyces lividans TK21, J Bacteriol, 170, 1631, 10.1128/JB.170.4.1631-1636.1988

Taschke, 1986, Analysis of transcription and processing signals of the 16S–23S rRNA operon of Mycoplasma hyopneumoniae, Mol & Gen Genet, 205, 434, 10.1007/BF00338079

Thiele, 1994, The 16S/23S ribosomal spacer region of Coxiella burnetii, Eur J Epidemiol, 10, 421, 10.1007/BF01719666

Thompson, 1994, clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalities and weight matrix choice, Nucleic Acids Res, 22, 4673, 10.1093/nar/22.22.4673

Towner, 1993, Molecular Methods for Microbial Identification and Typing, 10.1007/978-94-011-1506-3

Uemori, 1992, Amplification of the 16S–23S spacer region in rRNA operons of Mycoplasmas by the polymerase chain reaction, Syst Appl Microbiol, 15, 181, 10.1016/S0723-2020(11)80089-5

Vaneechoutte, 1992, Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA), FEMS Microbiol Lett, 93, 227, 10.1111/j.1574-6968.1992.tb05102.x

Wartell, 1990, Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis, Nucleic Acids Res, 18, 2699, 10.1093/nar/18.9.2699

Waterhouse, 1993, Differences in the hybridization pattern of Bacillus subtilis genes coding for rRNA depend on the method of DNA preparation, Appl Environ Microbiol, 59, 919, 10.1128/AEM.59.3.919-921.1993

Watson, 1953, Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid, Nature, 171, 737, 10.1038/171737a0

Watson, 1987, Molecular Biology of the Gene

Weisburg, 1991, 16S ribosomal DNA amplification for phylogenetic study, J Bacteriol, 173, 697, 10.1128/JB.173.2.697-703.1991

Whiley, 1995, Heterogeneity among 16S–23S rRNA intergenic spacers of species within the ‘Streptococcus milleri group’, Microbiology, 141, 1461, 10.1099/13500872-141-6-1461

de Wit, 1994, Mycobacterium leprae isolates from different sources have identical sequences of the spacer region between the 16S and 23S ribosomal RNA genes, Microbiology, 140, 1983, 10.1099/13500872-140-8-1983

Woese, 1987, Bacterial evolution, Microbiol Rev, 51, 221, 10.1128/MR.51.2.221-271.1987

Young, 1979, Sequence of the 16S–23S spacer region in two ribosomal RNA operons of Escherichia coli, J Biol Chem, 254, 3264, 10.1016/S0021-9258(18)50754-7

Yu, 1982, Molecular cloning of the ribosomal RNA genes of the photosynthetic bacterium Rhodopseudomonas capsulata, Mol & Gen Genet, 188, 392, 10.1007/BF00330039