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

References

1. Abed Y., Boilet C., De Micco P. 1995a; Demonstration of Mycobacterium kansasii species heterogeneity by the amplification of the 16S–23S spacer region. J Med Microbiol A3:156–158
   [Google Scholar]
2. Abed Y., Davin-Regli A., Boilet C., De Micco P. 1995b; Efficient discrimination of Mycobacterium tuberculosis strains by 16S–23S spacer region-based random amplified polymorphic DNA analysis. J Clin Microbiol 33:1418–1420
   [Google Scholar]
3. Amann R. I., Ludwig W., Schleifer K.-H. 1995; Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
   [Google Scholar]
4. Amikam D., Glaser G., Razin S. 1984; Mycoplasmas (Mollicutes) have a low number of rRNA genes. J Bacteriol 158:376–378
   [Google Scholar]
5. Andresson O. S., Fridjdnsson O. H. 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 176:6165–6169
   [Google Scholar]
6. Auriol J., Guesdon J. L, Guibourdenche M., Riou J. Y. 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 10:219–226
   [Google Scholar]
7. Bacot C. M., Reeves R. H. 1991; Novel tRNA gene organization in the 16S–23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster. J Bacteriol 173:4234–4236
   [Google Scholar]
8. Barry T, Colleran G, Glennon M., Dunican L. K., Gannon F. 1991; The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria PCR. Methods Appl 1:51–56
   [Google Scholar]
9. Bercovier H., Kafri O., Sela S. 1986; Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem Biophys Res Commun 136:1136–1141
   [Google Scholar]
10. Bourque S. N., Valero J. R., Lavoie M. C., Levesque R. C. 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 61:1623–1626
    [Google Scholar]
11. Brosius J., Dull T. J., Noller H. F. 1980; Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 77:201–204
    [Google Scholar]
12. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. 1981; Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107–127
    [Google Scholar]
13. Campbell K. D., East A. K., Thompson D. E., Collins M. D. 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 144:171–180
    [Google Scholar]
14. Cartwright C. P., Stock F., Beekman S. E., Williams E. C., Gill V. J. 1995; PCR amplification of rRNA intergenic spacer regions as a method for epidemiologic typing of Clostridium difficile. J Clin Microbiol 33:184–187
    [Google Scholar]
15. Dasen S. E., LiPuma J. J., Kostman J. R., Stull T. L. 1994; Characterization of PCR-ribotyping for Burkhoideria (Pseudomonas) cepacia. J Clin Microbiol 32:2422–2424
    [Google Scholar]
16. Dolzani L, Tonin E., Lagatolla C., Monti-Bragadin C. 1994; Typing of Staphylococcus aureus by amplification of the 16S–23S rRNA intergenic spacer sequences. FEMS Microbiol Lett 119:167–174
    [Google Scholar]
17. Dolzani L, Tonin E., Lagatolla C, Prandin L, Monti-Bragadin C. 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 33:1108–1113
    [Google Scholar]
18. Dryden S. C., Kaplan S. 1990; Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucleic Acids Res 18:7267–7277
    [Google Scholar]
19. East A. K., Collins M. D. 1993; Molecular characterization of DNA encoding 23S rRNA and 16S–23S rRNA intergenic spacer regions of Aeromonas hydrophila. FEMS Microbiol Lett 106:129–134
    [Google Scholar]
20. East A. K., Allaway D., Collins M. D. 1992; Analysis of DNA encoding 23S rRNA and 16S–23S rRNA intergenic spacer regions from Plesiomonas shigelloides. FEMS Microbiol Lett 74:57–62
    [Google Scholar]
21. Emond E., Fliss I, Pandian S. 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 59:2690–2697
    [Google Scholar]
22. Feingold J, Bellofatto V, Shapiro L, Amemiya K. 1985; Organization and nucleotide sequence analysis of an rRNA and tRNA gene cluster from Caulobacter crescentus. J Bacteriol 163:155–166
    [Google Scholar]
23. Fleischmann R. D. others 1995; Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512
    [Google Scholar]
24. Frothingham R., Wilson K. H. 1993; Sequence-based differentiation of strains in the Mycobacterium avium complex. J Bacteriol 175:2818–2825
    [Google Scholar]
25. Frothingham R., Wilson K. H. 1994; Molecular phylogeny of the Mycobacterium avium complex demonstrates clinically meaningful divisions. J Infect Dis 169:305–312
    [Google Scholar]
26. Gamier T., Canard B., Cole S. T. 1991; Cloning, mapping, and molecular characterization of the rRNA operons of Clostridium perfringens. J Bacteriol 173:5431–5438
    [Google Scholar]
27. van der Giessen J. W. B., Haring R. M., van der Zeijst B. A. M. 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 140:1103–1108
    [Google Scholar]
28. Gill S., Belles-Isles J, Brown G, Gagne S., Lemieux C, Mercier J. P., Dion P. 1994; Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates. Can J Microbiol 40:541–547
    [Google Scholar]
29. Glennon M., Smith T., Cormican M, Noone D, Barry T, Maher M, Dawson M., Gilmartin J. J., Gannon F. 1994; The ribosomal intergenic spacer region: a target for the PCR based diagnosis of tuberculosis. Tubercle Lung Dis 75:353–360
    [Google Scholar]
30. Green C. J., Stewart G. C, Hollis M. A., Void B. S., Bott K. F. 1985; Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB. Gene 37:261–266
    [Google Scholar]
31. Griffen A. L, Leys E. J., Fuerst P. A. 1992; Strain identification of Actinobacillus actinomycetemcomitans using the polymerase chain reaction. Oral Microbiol Immunol 7:240–243
    [Google Scholar]
32. Gürtler V. 1993; Typing of Clostridium difficile strains by PCR-amplification of variable length 16S–23S rDNA spacer regions. J Gen Microbiol 139:3089–3097
    [Google Scholar]
33. Gürtler V., Barrie H. D. 1995; Typing of Staphylococcus aureus strains by PCR-amplification of variable length 16S–23S rDNA spacer regions: characterization of spacer sequences. Microbiology 141:1255–1265
    [Google Scholar]
34. Hall L. M. C. 1994; Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria?. Microbiology 140:197–204
    [Google Scholar]
35. Harasawa R, Mizusawa H, Nozawa K, Nakagawa T, Asada K., Kato I. 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 144:489–493
    [Google Scholar]
36. Harvey S., Hill C. W., Squires C., Squires C. L. 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 170:1235–1238
    [Google Scholar]
37. Hookey J. V., Birtles R. J., Saunders N. A. 1995; Intergenic 16S rRNA gene (rDNA)-23S rDNA sequence length polymorphisms in members of the family Legionellaceae. J Clin Microbiol 33:2377–2381
    [Google Scholar]
38. Iwami M, Muto A, Yamao F., Osawa S. 1984; Nucleotide sequence of the rrnB 16S ribosomal RNA gene from Mycoplasma capricolum. Mol & Gen Genet 196:317–322
    [Google Scholar]
39. Jannes G, Vaneechoutte M, Lannoo M, Gillis M, Vancanneyt M, Vandamme P, Verschraegen G., Van Heuverswyn H., Rossau R. 1993; Polyphasic taxonomy leading to the proposal of Moraxella canis sp. nov. for Moraxella catarrhalis-like strains. Int J Syst Bacteriol 43:438–449
    [Google Scholar]
40. Jarsch M., Bock A. 1983; DNA sequence of the 16S rRNA/23S rRNA intercistronic spacer of two rDNA operons of the archae-bacterium Methanococcus vannielii. Nucleic Acids Res 11:7537–7544
    [Google Scholar]
41. Jensen M. A., Straus N. 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 3:186–194
    [Google Scholar]
42. Jensen M. A., Webster J. A., Straus N. 1993; Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59:945–952
    [Google Scholar]
43. Kim E., Kim H., Hong S. P., Kang K. H., Kho Y. H., Park Y. H. 1993; Gene organization and primary structure of a ribosomal RNA gene cluster from Streptomyces griseus subsp. griseus. Gene 132:21–31
    [Google Scholar]
44. Kjems J, Leffers H, Garrett R. A., Wich G., Leinfelder W., Bdck A. 1987; Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archae-bacterium Thermoproteus tenax. Nucleic Acids Res 15:4821–4835
    [Google Scholar]
45. Kostman J. R., Edlind T. D., LiPuma J. J., Stull T. L. 1992; Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol 30:2084–2087
    [Google Scholar]
46. Kostman J. R., Alden M. B., Mair M., Edlind T. D., LiPuma J. J., Stull T. L. 1995; A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J Infect Dis 171:204–208
    [Google Scholar]
47. Kuske C. R., Kirkpatrick B. C. 1992; Phylogenetic relationships between the western aster yellows mycoplasmalike organism and other prokaryotes established by 16S rRNA gene sequence. Int J Syst Bacteriol 42:226–233
    [Google Scholar]
48. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. J., Pace N. R. 1985; Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959
    [Google Scholar]
49. Leys E. J., Griffen A. L, Strong S. J., Fuerst P. A. 1994; Detection and strain identification of Actinobacillus actinomycetemcomitans by nested PCR. J Clin Microbiol 32:1288–1294
    [Google Scholar]
50. Liveris D., Gazumyan A., Schwartz I. 1995; Molecular typing of Borrelia burgdorferi sensu lato by PCR-restriction fragment length polymorphism analysis. J Clin Microbiol 33:589–595
    [Google Scholar]
51. Loughney K., Lund E., Dahlberg J. E. 1982; tRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis. Nucleic Acids Res 10:1607–1624
    [Google Scholar]
52. Ludwig W, Kirchof G, Klugbauer N, Weizenegger N, Betzl D, Ehrmann M, Hertel C, Jilg S, Tatzel R, Zitzelsberger H, Liebl S, Hochberger M, Shah J, Lane D., Wallnoef P. R. 1992; Complete 23 S ribosomal RNA sequences of gram-positive bacteria with a low DNA G + C content. Syst Appl Microbiol 15:487–501
    [Google Scholar]
53. McLaughlin G. L, Howe D. K., Biggs D. R., Smith A. R., Ludwinski P., Fox B. C, Tripathy D. N., Frasch C. E., Wenger J. D., Carey R. B., Hassan-King M., Vodkin M. H. 1993; Amplification of rDNA loci to detect and type Neisseria meningitidis and other eubacteria. Mol Cell Probes 7:7–17
    [Google Scholar]
54. Maddison W. P., Maddison D. R. 1992 MacClade: Analysis of Phytogeny and Character Evolution. Version 3.0 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
55. Marconi R. T., Liveris D., Schwartz I. 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 33:2427–2434
    [Google Scholar]
56. Martirosian G, Kuijpers S, Verbrugh H., van Belkum A., Meisel-Mikolajczyk F. 1995; PCR ribotyping and arbitrarily primed PCR for typing strains of Clostridium difficile from a Polish maternity hospital. J Clin Microbiol 33:2016–2021
    [Google Scholar]
57. Matar G. M., Swaminathan B., Hunter S. B., Slater L. N., Welch D. F. 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 31:1730–1734
    [Google Scholar]
58. Minnick M. F., Strange J. C., Williams K. F. 1994; Characterization of the 16S–23S rRNA intergenic spacer of Bartonella bacilliformis. Gene 143:149–150
    [Google Scholar]
59. Morgan E. A., Ikemura T., Nomura M. 1977; Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli. Proc Natl Acad Sci USA 74:2710–2714
    [Google Scholar]
60. Mullis K. B., Faloona F. A. 1987; Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods Enzymol 155:335–350
    [Google Scholar]
61. Nakagawa T, Uemori T, Asada K., Kato I., Harasawa R. 1992; Acholeplasma laidlawii has tRNA genes in the 16S–23S spacer of the rRNA operon. J Bacteriol 174:8163–8165
    [Google Scholar]
62. Nakagawa T, Shimada M, Mukai H, Asada K, Kato I., Fujino K., Sato T. 1994; Detection of alcohol-tolerant hiochi bacteria by PCR. Appl Environ Microbiol 60:637–640
    [Google Scholar]
63. Nastasi A., Mammina C. 1995; Epidemiological evaluation by PCR ribotyping of sporadic and outbreak-associated strains of Salmonella enterica serotype Typhimurium. Res Microbiol 146:99–106
    [Google Scholar]
64. Navarro E, Simonet P, Normand P., Bardin R. 1992; Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol 151:107–115
    [Google Scholar]
65. Neefs J.-M., Van De Peer Y., Hendriks L., De Wachter R. 1990; Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 18:2237–2317
    [Google Scholar]
66. Normand P, Cournoyer B, Simonet P., Nazaret S. 1992; Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene 111:119–124
    [Google Scholar]
67. Nour S. M., Cleyet-Marel J.-C., Beck D., Effosse A., Fernandez M. P. 1994; Genotypic and phenotypic diversity of Rhizobium isolated from chickpea (Cicer arietinum L.). Can J Microbiol 40:345–354
    [Google Scholar]
68. Nowak A., Burkiewicz A., Kur J. 1995; PCR differentiation of seventeen genospecies of Acinetobacter. FEMS Microbiol Lett 126:181–188
    [Google Scholar]
69. Olsen G. J., Pace N. R., Nuell M., Kaine B. P., Gupta R., Woese C. R. 1985; Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications. J Mol Evol 22:301–307
    [Google Scholar]
70. Olsen G. J., Larsen N., Woese C. R. 1991; The ribosomal RNA database project. Nucleic Acids Res 19:suppl2017–2021
    [Google Scholar]
71. Pernodet J.-L, Boccard F., Alegre M.-T., Gagnat J., Guerineau M. 1989; Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene 79:33–46
    [Google Scholar]
72. Ponsonnet C., Nesme X. 1994; Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 161:300–309
    [Google Scholar]
73. Rossau R, Michielsen A, Jannes G, Duhamel M, Kersters K., van Heuverswyn H. 1992; DNA probes for Bordetella species and a colorimetric reverse hybridization assay for the detection of Bordetella pertussis. Mol Cell Probes 6:281–289
    [Google Scholar]
74. Roux V., Raoult D. 1995a; Inter- and intraspecies identification of Bartonella (Rochalimaea) species. J Clin Microbiol 33:1573–1579
    [Google Scholar]
75. Roux V., Raoult D. 1995b; The 16S–23S rRNA intergenic spacer region of Bartonella (Rochalimaea) species is longer than usually described in other bacteria. Gene 156:107–111
    [Google Scholar]
76. Sagredo B., Jedlicki E., Orellana O. 1992; Organization of the 16S–23S intergenic spacer region of the two rRNA operons from Thiobacillus ferooxidans. Geomicrobiol J 10:239–247
    [Google Scholar]
77. Salzano G, Moschetti G, Villani F, Pepe O, Mauriello G., Coppola S. 1994; Genotyping of Streptococcus thermophilus evidenced by restriction analysis of ribosomal DNA. Res Microbiol 145:651–658
    [Google Scholar]
78. Sawada M, Muto A, Iwami M., Yamao F., Osawa S. 1984; Organization of ribosomal RNA genes in Mycoplasma capricolum. Mol & Gen Genet 196:311–316
    [Google Scholar]
79. Sechi L. A., Daneo-Moore L. 1993; Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC 9790. J Bacteriol 175:3213–3219
    [Google Scholar]
80. Sheffield V. C, Cox D. R., Lerman L. S., Myers R. M. 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 86:232–236
    [Google Scholar]
81. Smith-Vaughan H. C, Sriprakash K. S., Mathews J. D., Kemp D. J. 1995; Long PCR-ribotyping of nontypable Haemophilus influenzae. J Clin Microbiol 33:1192–1195
    [Google Scholar]
82. Suzuki Y, Ono Y, Nagata A., Yamada T. 1988; Molecular cloning and characterization of an rRNA operon in Streptomyces lividans TK21. J Bacteriol 170:1631–1636
    [Google Scholar]
83. Taschke C., Herrmann R. 1986; Analysis of transcription and processing signals of the 16S–23S rRNA operon of Mycoplasma hyopneumoniae. Mol & Gen Genet 205:434–441
    [Google Scholar]
84. Thiele D., Willems H., Krauss H. 1994; The 16S/23S ribosomal spacer region of Coxiella burnetii. Eur J Epidemiol 10:421–426
    [Google Scholar]
85. Thompson J. D., Higgins D. G., Gibson T. J. 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 22:4673–4680
    [Google Scholar]
86. Towner K. J., Cockayne A. 1993 Molecular Methods for Microbial Identification and Typing London: Chapman & Hall;
    [Google Scholar]
87. Uemori T, Asada K, Kato I., Harasawa R. 1992; Amplification of the 16S–23S spacer region in rRNA operons of Mycoplasmas by the polymerase chain reaction. Syst Appl Microbiol 15:181–186
    [Google Scholar]
88. Vaneechoutte M, Rossau R, De Vos P, Gillis M, Janssens D, Paepe N, De Rouck A, Fiers T, Claeys G., Kersters K. 1992; Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol Lett 93:227–234
    [Google Scholar]
89. Wartell R. M., Hosseini S. H., Moran C. P. 1990; Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis. Nucleic Acids Res 18:2699–2705
    [Google Scholar]
90. Waterhouse R. N., Glover L. A. 1993; Differences in the hybridization pattern of Bacillus subtilis genes coding for rRNA depend on the method of DNA preparation. Appl Environ Microbiol 59:919–921
    [Google Scholar]
91. Watson J. D., Crick F. H. C. 1953; Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–738
    [Google Scholar]
92. Watson J. D., Hopkins N. H., Roberts J. W., Steitz J. A., Weiner A. M. 1987 Molecular Biology of the Gene Menlo Park, CA: The Benjamin/Cummings Publishing Company;
    [Google Scholar]
93. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
    [Google Scholar]
94. Whiley R. A., Duke B., Hardie J. M., Hall L. M. C. 1995; Heterogeneity among 16S–23S rRNA intergenic spacers of species within the ‘Streptococcus milleri group’. Microbiology 141:1461–1467
    [Google Scholar]
95. de Wit M. Y. L., Klatser P. R. 1994; Mycobacterium leprae isolates from different sources have identical sequences of the spacer region between the 16S and 23S ribosomal RNA genes. Microbiology 140:1983–1987
    [Google Scholar]
96. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
    [Google Scholar]
97. Young R. A., Macklis R., Steitz J. A. 1979; Sequence of the 16S–23S spacer region in two ribosomal RNA operons of Escherichia coli. J Biol Chem 254:3264–3271
    [Google Scholar]
98. Yu P.-L, Hohn B., Falk H., Drews G. 1982; Molecular cloning of the ribosomal RNA genes of the photosynthetic bacterium Rhodopseudomonas capsulata. Mol & Gen Genet 188:392–398
    [Google Scholar]