DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates

Microbiology

Volumn 145, Issue 7, 1999, Pages 1785-1796

  Gürtler, Volker ^a   Yujun, Rao ^a   Pearson, Stephen R ^a   Bates, Susan M ^a   Mayall, Barrie C ^a  

^a AUSTIN HEALTH   (Australia)

Author keywords

Concerted evolution; Enterococcus faecalis; Heteroduplex; Homoduplex; Long intergenic 16S 23S rDNA spacer region

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; SPACER DNA;

ALLELE; ARTICLE; BACTERIUM ISOLATE; DNA SEQUENCE; ENTEROCOCCUS FAECALIS; GEL ELECTROPHORESIS; GENETIC HETEROGENEITY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ENTEROCOCCUS FAECALIS;

EID: 0032805303     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/13500872-145-7-1785     Document Type: Article

References (52)

1. Antón, A. I., Martínez-Murcia, A. J. & Rodríguez-Valera, F. (1998). Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J Mol Evol 47, 62-72.
2. Arthur, M., Reynolds, P. & Courvalin, P. (1996). Glycopeptide resistance in enterococci. Trends Microbiol 4, 401-407.
3. Bell, J. M., Paton, J. C. & Turnidge. J. (1998). Emergence of vancomycin-resistant enterococci in Australia - phenotypic and genotypic characteristics. J Clin Microbiol 36, 2187-2190.
4. Cilia, V., Lafay, B. & Christen, R. (1996). Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13, 451-461.
5. Cremonesi, L., Carrera, P., Fumagalli, A. & 7 other authors (1999). Validation of double gradient denaturing gradient gel electrophoresis through multigenic retrospective analysis. Clin Chem 45, 35-10.
6. Dover, G. (1982). Molecular drive: a cohesive mode of species evolution. Nature 299, 111-117.
7. Dunne, W. M., Jr & Wang. W. (1997). Clonal dissemination and colony morphotype variation of vancomycin-resistant Enterococcus faecium isolates in metropolitan Detroit, Michigan. J Clin Microbiol 35, 388-392.
8. Facklam, R. R. & Collins, M. D. (1989). Identification of Enterococcus species isolated from human infections by a conventional test scheme. J Clin Microbiol 27, 731-734.
9. Ganguly, A., Rock, M. J. & Prockop, D. J. (1993). Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes. Proc Natl head Sci USA 90, 10325-10329.
10. García-Martínez, J., Martínez-Murcia, A. J., Rodríguez-Valera, F. & Zorraquino, A. (1996a). Molecular evidence supporting the existence of two major groups in uropathogenic Escherichia coli. FEMS Immunol Med Microbiol 14, 231-244.
11. García-Martínez, J., Martínez-Murcia, A., Antón, A. I. & Rodriguez-Valera, F. (1996b). Comparison of the small 16S to 23S intergenic spacer region (ISR) of the rRNA operons of some Escherichia coli strains of the ECOR collection and E. coli K-12. J Bacteriol 178, 6374-6377.
12. 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.
13. 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.
14. Gürtler, V. & Mayall, B. C. (1999). rDNA spacer rearrangements and concerted evolution. Microbiology 145, 2-3.
15. Gürtler, V. & Stanisich, V. A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
16. Gürtler, V., Wilson, V. A. & Mayall, B. C. (1991). Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol 137, 2673-2679.
17. Hall, L. (1994). Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria? Microbiology 140, 197-204.
18. Ke, S. H. & Wartell, R. M. (1995). Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment. Biochemistry 34, 4593-4600.
19. Körkkö, J., Annunen, S., Pihlajamaa, T., Prockop, D. J. & AlaKokko, L. (1998). Conformation sensitive gel electrophoresis for simple and accurate detection of mutations: comparison with denaturing gradient gel electrophoresis and nucleotide sequencing. Proc Natl Acad Sci USA 95, 1681-1685.
20. Lan, R. & Reeves, P. R. (1998). Recombination between rRNA operons created most of the ribotype variation observed in the seventh pandemic clone of Vibrio cholerae. Microbiology 144, 1213-1221.
21. Leblond, P. & Decaris, B. (1998). Chromosome geometry and intraspecific genetic polymorphism in Gram-positive bacteria revealed by pulsed-field gel electrophoresis. Electrophoresis 19, 582-588.
22. Lerman, L. S., Silverstein, K. & Grinfeld, E. (1986). Searching for gene defects by denaturing gradient gel electrophoresis. Cold Spring Harbor Symp Quant Biol 51, 285-297.
23. Liu, S. L. & Sanderson, K. E. (1995). Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci USA 92, 1018-1022.
24. Liu, S. L. & Sanderson, K. E. (1996). Highly plastic chromosomal organization in Salmonella typhi. Proc Natl Acad Sci USA 93, 10303-10308.
25. Liu, S. L., Hessel, A. & Sanderson, K. E. (1993). Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci USA 90, 6874-6878.
26. Miele, A., Bandera, M. & Goldstein, B. P. (1995). Use of primers selective for vancomycin resistance genes to determine van genotype in enterococci and to study gene organization in VanA isolates. Antimicrob Agents Chemother 39, 1772-1778.
27. Monstein, H. J., Quednau, M., Samuelsson, A., Ahrné, S., Isaksson, B. & Jonasson, J. (1998). Division of the genus Enterococcus into species groups using PCR-based molecular typing methods. Microbiology 144, 1171-1179.
28. Murray, B. E. (1990). The life and times of the Enterococcus. Clin Microbiol Rev 3, 46-65.
29. Murray, B. F., Singh, K. V., Ross, R. P., Heath, J. D., Dunny, G. M. & Weinstock, G. M. (1993). Generation of restriction map of Enterococcus faecalis OG1 and investigation of growth requirements and regions encoding biosynthetic function. J Bacteriol 175, 5216-5223.
30. Myers, R. M. & Maniatis, T. (1986). Recent advances in the development of methods for detecting single-base substitutions associated with human genetic diseases. Cold Spring Harbor Symp Quant Biol 51, 275-284.
31. Myers, R. M., Fischer, S. G., Lerman, L. S. & Maniatis, T. (1985a). Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13, 3131-3145.
32. Myers, R. M., Fischer, S. G., Maniatis, T. & Lerman, L. S. (1985b). Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Res 13, 3111-3129.
33. Myers, R. M., Maniatis, T. & Lerman, L. S. (1987). Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155, 501-527.
34. Naïmi, A., Beck, G. & Branlant, C. (1997). Primary and secondary structures of rRNA spacer regions in enterococci. Microbiology 143, 823-834.
35. Ninet, B., Monod, M., Emler, S., Pawlowski, J., Metral, C., Rohner, P., Auckenthaler, R. & Hirschel, B. (1996). Two different 16S rRNA genes in a mycobacterial strain. J Clin Microbiol 34, 2531-2536.
36. Patel, R., Uhl, J. R., Kohner, P., Hopkins, M. K. & Cockerill, F. R., 3rd (1997). Multiplex PCR detection of vanA, vanB, vanC-1, and vanC-2/3 genes in enterococci. J Clin Microbiol 35, 703-707.
37. Patel, R., Piper, K. E., Rouse, M. S., Steckelberg, J. M., Uhl, J. R., Kohner, P., Hopkins, M. K., Cockerill, F. R., 3rd & Kline, B. C. (1998). Determination of 16S rRNA sequences of enterococci and application to species identification of nonmotile Enterococcus gallinarum isolates. J Clin Microbiol 36, 3399-3407.
38. Pegues, D. A., Pegues, C. F., Hibberd, P. L., Ford, D. S. & Hooper, D. C. (1997). Emergence and dissemination of a highly vancomycin-resistant vanA strain of Enterococcus faecium at a large teaching hospital. J Clin Microbiol 35, 1565-1570.
39. Perez-Luz, S., Rodriguez-Valera, F., Lan, R. & Reeves, P. R. (1998). Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. J Bacteriol 180, 2144-2151.
40. Poland, D. (1974). Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations. Biopolymers 13, 1859-1871.
41. Reischl, U., Feldmann, K., Naumann, L., Gaugier, B. J., Ninet, B., Hirschel, B. & Emler, S. (1998). 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J Clin Microbiol 36, 1761-1764.
42. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74, 5463-5467.
43. Schleifer, K. H. & Kilpper-Bälz (1984). Transfer of Streptococcus faecalis and Streptococcus faecium to the genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. Int J Syst Bacteriol 34, 31-34.
44. Schleifer, K. H. & Kilpper-Bälz, R. (1987). Molecular and chemotaxonomic approaches to the classification of Streptococci, Enterococci and Lactococci: A review. Syst Appl Microbiol 10, 1-19.
45. 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.
46. 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.
47. 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 penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
48. Tyrrell, G. J., Bethune, R. N., Willey, B. & Low, D. E. (1997). Species identification of enterococci via intergenic ribosomal PCR. J Clin Microbiol 35, 1054-1060.
49. Uttley, A. H., Collins, C. H., Naidoo, J. & George, R. C. (1988). Vancomycin-resistant enterococci. Lancet 1, 57-58.
50. Wang, Y., Zhang, Z. & Ramanan, N. (1997). The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179, 3270-3276.
51. Williams, A. M., Rodrigues, U. M. & Collins, M. D. (1991). Intrageneric relationships of Enterococci as determined by reverse transcriptase sequencing of small-subunit rRNA. Res Microbiol 142, 67-74.
52. Zimmer, E. A., Martin. S. L., Beverley, S. M., Kan, Y. W. & Wilson, A. C. (1980). Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc Natl Acad Sci USA 11, 2158-2162.