Detection of human intestinal catalase-negative, gram-positive cocci by rRNA-targeted reverse transcription-PCR

Applied and Environmental Microbiology

Volumn 76, Issue 16, 2010, Pages 5440-5451

  Kubota, Hiroyuki ^a   Tsuji, Hirokazu ^a   Matsuda, Kazunori ^a   Kurakawa, Takashi ^a   Asahara, Takashi ^a   Nomoto, Koji ^a  

^a YAKULT CENTRAL INSTITUTE FOR MICROBIOLOGICAL RESEARCH   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL SYSTEMS; DETECTION LIMITS; FECAL SAMPLES; GRAM-POSITIVE COCCI; LACTOCOCCUS; POPULATION LEVELS; PRIMER SETS; QUANTITATIVE PCR; REVERSE TRANSCRIPTION; SPECIFIC PRIMERS; STANDARD DEVIATION;

RNA; TRANSCRIPTION;

POLYMERASE CHAIN REACTION;

BACTERIAL RNA; CATALASE; PRIMER DNA; RNA 16S; RNA 23S;

BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ANALYSIS; POLYMERASE CHAIN REACTION; REAL TIME;

ARTICLE; BACTERIAL COUNT; ENZYMOLOGY; EVALUATION; FECES; GENETICS; GRAM POSITIVE COCCI; HUMAN; INTESTINE; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; EVALUATION STUDY; PROCEDURES;

CATALASE; COLONY COUNT, MICROBIAL; DNA PRIMERS; FECES; GRAM-POSITIVE COCCI; HUMANS; INTESTINES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SENSITIVITY AND SPECIFICITY;

ENTEROCOCCUS; ENTEROCOCCUS AVIUM; ENTEROCOCCUS CACCAE; ENTEROCOCCUS CASSELIFLAVUS; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS FAECIUM; LACTOCOCCUS; LACTOCOCCUS GARVIEAE; LACTOCOCCUS LACTIS SUBSP. CREMORIS; LACTOCOCCUS LACTIS SUBSP. LACTIS; LACTOCOCCUS PISCIUM; LACTOCOCCUS PLANTARUM; POSIBACTERIA; STREPTOCOCCUS; STREPTOCOCCUS SALIVARIUS;

EID: 77955959302     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03132-09     Document Type: Article

References (71)

1. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, andD. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
2. Andersson, A. F., M. Lindberg, H. Jakobsson, F. Backhed, P. Nyren, andL. Engstrand. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. FLoS One 3:e2836.
3. Balamurugan, R., E. Rajendiran, S. George, G. V. Samuel, andB. S. Ramakrishna. 2008. Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer. J. Gastroenterol. Hepatol. 23:1298-1303.
4. Bartosch, S., A. Fite, G. T. Macfarlane, andM. E. McMurdo. 2004. Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl. Environ. Microbiol. 70: 3575-3581.
5. Benno, Y., K. Endo, T. Mizutani, Y. Namba, T. Komori, andT. Mitsuoka. 1989. Comparison of fecal microflora of elderly persons in rural and urban areas of Japan. Appl. Environ. Microbiol. 55:1100-1105.
6. Beresford, T. P., N. A. Fitzsimons, N. L. Brennan, andT. M. Cogan. 2001. Recent advances in cheese microbiology. Int. Dairy J. 11:259-274.
7. Bosshard, P. P., S. Abels, M. Altwegg, E. C. Bottger, andR. Zbinden. 2004. Comparison of conventional and molecular methods for identification of aerobic catalase-negative gram-positive cocci in the clinical laboratory. J. Clin. Microbiol. 42:2065-2073.
8. Casalta, E., andM. C. Montel. 2008. Safety assessment of dairy microorganisms: the Lactococcus genus. Int. J. Food Microbiol. 126:271-273.
9. Claesson, M. J., O. O'Sullivan, Q. Wang, J. Nikkila, J. R. Marchesi, H. Smidt, W. M. de Vos, R. P. Ross, and P. W. O'Toole. 2009. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. FLoS One 4:e6669.
10. Cogan, T. M., M. Barbosa, E. Beuvier, B. Bianchi-Salvadori, P. S. Cocconcelli, I. Fernandes, J. Gomez, R. Gomes, G. Kalantzopoulos, A. Ledda, M. Medina, M. C. Rea, andE. Rodriguez. 1997. Characterization of the lactic acid bacteria in artisanal dairy products. J. Dairy Res. 64:409-421.
11. de Bruin, M. A., andL. W. Riley. 2007. Does vancomycin prescribing intervention affect vancomycin-resistant Enterococcus infection and colonization in hospitals? A systematic review. BMC Infect. Dis. 7:24.
12. Dethlefsen, L., S. Huse, M. L. Sogin, andD. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:e280.
13. Dumonceaux, T. J., J. E. Hill, S. A. Briggs, K. K. Amoako, S. M. Hemmingsen, andA. G. Van Kessel. 2006. Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target. J. Microbiol. Methods 64:46-62.
14. Easmon, C. S., A. Tanna, P. Munday, andS. Dawson. 1981. Group B streptococci-gastrointestinal organisms? J. Clin. Pathol. 34:921-923.
15. Emori, T. G., andR. P. Gaynes. 1993. An overview of nosocomial infections, including the role of the microbiology laboratory. Clin. Microbiol. Rev. 6:428-442.
16. Facklam, R. 2002. What happened to the streptococci: overview of taxonomie and nomenclature changes. Clin. Microbiol. Rev. 15:613-630.
17. Facklam, R. R., andM. D. Collins. 1989. Identification of Enterococcus species isolated from human infections by a conventional test scheme. J. Clin. Microbiol. 27:731-734.
18. Finegold, S. M., V. L. Sutter, P. T. Sugihara, H. A. Elder, S. M. Lehmann, and R. L. Phillips. 1977. Fecal microbial flora in Seventh Day Adventist populations and control subjects. Am. J. Clin. Nutr. 30:1781-1792.
19. Firmesse, O., E. Alvaro, A. Mogenet, J. L. Bresson, R. Lemee, P. Le Ruyet, C. Bonhomme, D. Lambert, C. Andrieux, J. Dore, G. Corthier, J. P. Furet, andL. Rigottier-Gois. 2008. Fate and effects of Camembert cheese microorganisms in the human colonic microbiota of healthy volunteers after regular Camembert consumption. Int. J. Food Microbiol. 125:176-181.
20. Firmesse, O., S. Rabot, L. G. Bermudez-Humaran, G. Corthier, andJ. P. Furet. 2007. Consumption of Camembert cheese stimulates commensal enterococci in healthy human intestinal microbiota. FEMS Microbiol. Lett. 276:189-192.
21. Furet, J. P., P. Quenee, andP. Tailliez. 2004. Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR. Int. J. Food Microbiol. 97:197-207.
22. Gelsomino, R., M. Vancanneyt, T. M. Cogan, andJ. Swings. 2003. Effect of raw-milk cheese consumption on the enterococcal flora of human feces. Appl. Environ. Microbiol. 69:312-319.
23. Gilmore, M. S., D. B. Clewell, P. Courvalin, G. M. Dunny, B. E. Murray, andL. B. Rice. 2002. The enterococci: pathogenesis, molecular biology, and antibiotic resistance. ASM. Press, Washington, DC.
24. Gourse, R. L., T. Gaal, M. S. Bartlett, J. A. Appleman, andW. Ross. 1996. rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. Annu. Rev. Microbiol. 50:645-677.
25. Grattepanche, F., C. Lacroix, P. Audet, andG. Lapointe. 2005. Quantification by real-time PCR of Lactococcus lactis subsp. cremoris in milk fermented by a mixed culture. Appl. Microbiol. Biotechnol. 66:414-421.
26. Greiner, O., P. J. Day, P. P. Bosshard, F. Imeri, M. Altwegg, andD. Nadal. 2001. Quantitative detection of Streptococcus pneumoniae in nasopharyngeal secretions by real-time PCR. J. Clin. Microbiol. 39:3129-3134.
27. Gueimonde, M., S. Tolkko, T. Korpimaki, andS. Salminen. 2004. New real-time quantitative PCR procedure for quantification of bifidobacteria in human fecal samples. Appl. Environ. Microbiol. 70:4165-4169.
28. Haarman, M., andJ. Knol. 2006. Quantitative real-time PCR analysis of fecal Lactobacillus species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 72:2359-2365.
29. Haarman, M., andJ. Knol. 2005. Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 71:2318-2324.
30. Hamilton-Miller, J. M., andS. Shah. 1999. Identification of clinically isolated vancomycin-resistant enterococci: comparison of API and BBL Crystal systems. J. Med. Microbiol. 48:695-696.
31. Hansen, S. M., N. Uldbjerg, M. Kilian, andU. B. Sorensen. 2004. Dynamics of Streptococcus agalactiae colonization in women during and after pregnancy and in their infants. J. Clin. Microbiol. 42:83-89.
32. Hayashi, H., R. Takahashi, T. Nishi, M. Sakamoto, andY. Benno. 2005. Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J. Med. Microbiol. 54:1093-1101.
33. He, J. W., andS. Jiang. 2005. Quantification of enterococci and human adenoviruses in environmental samples by real-time PCR. Appl. Environ. Microbiol. 71:2250-2255.
34. Islam, A. K., andE. Thomas. 1980. Faecal carriage of group B streptococci. J. Clin. Pathol. 33:1006-1008.
35. Jansen, G. J., A. C. Wildeboer-Veloo, R. H. Tonk, A. H. Franks, andG. W. Welling. 1999. Development and validation of an automated, microscopybased method for enumeration of groups of intestinal bacteria. J. Microbiol. Methods 37:215-221.
36. Jett, B. D., M. M. Huycke, andM. S. Gilmore. 1994. Virulence of enterococci. Clin. Microbiol. Rev. 7:462-478.
37. Kimoto-Nira, H., S. Ohmomo, M. Nomura, M. Kobayashi, K. Mizumahi, andT. Okamoto. 2008. Interference of in vitro and in vivo growth of several intestinal bacteria by Lactococcus strains. J. Microbiol. Biotechnol. 18:1286-1289.
38. Klyn, N., A. H. Weerkamp, andW. M. de Vos. 1995. Genetic marking of Lactococcus lactis shows its survival in the human gastrointestinal tract. Appl. Environ. Microbiol. 61:2771-2774.
39. Knudtson, L. M., andP. A. Hartman. 1992. Routine procedures for isolation and identification of enterococci and fecal streptococci. Appl. Environ. Microbiol. 58:3027-3031.
40. Leclercq, R., S. Dutka-Malen, J. Duval, andP. Courvalin. 1992. Vancomycin resistance gene vanC is specific to Enterococcus gallinarum. Antimicrob. Agents Chemother. 36:2005-2008.
41. Maruo, T., M. Sakamoto, T. Toda, andY. Benno. 2006. Monitoring the cell number of Lactococcus lactis subsp. cremoris FC in human feces by real-time PCR with strain-specific primers designed using the RAPD technique. Int. J. Food Microbiol. 110:69-76.
42. Matsuda, K., H. Tsuji, T. Asahara, Y. Kado, andK. Nomoto. 2007. Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR. Appl. Environ. Microbiol. 73:32-39.
43. Matsuda, K., H. Tsuji, T. Asahara, K. Matsumoto, T. Takada, andK. Nomoto. 2009. Establishment of an analytical system for the human fecal microbiota, based on reverse transcription-quantitative PCR targeting of multicopy rRNA molecules. Appl. Environ. Microbiol. 75:1961-1969.
44. Matsuki, T., K. Watanabe, J. Fujimoto, Y. Kado, T. Takada, K. Matsumoto, andR. Tanaka. 2004. Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl. Environ. Microbiol. 70:167-173.
45. Matsuki, T., K. Watanabe, J. Fujimoto, T. Takada, andR. Tanaka. 2004. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl. Environ. Microbiol. 70:7220-7228.
46. Mitchell, T. J. 2003. The pathogenesis of streptococcal infections: from tooth decay to meningitis. Nat. Rev. Microbiol. 1:219-230.
47. Mundy, L. M., D. F. Sahm, andM. Gilmore. 2000. Relationships between enterococcal virulence and antimicrobial resistance. Clin. Microbiol. Rev. 13:513-522.
48. Murray, B. E. 1990. The life and times of the Enterococcus. Clin. Microbiol. Rev. 3:46-65.
49. Navarro, F., andP. Courvalin. 1994. Analysis of genes encoding D-alanineD-alanine ligase-related enzymes in Enterococcus casseliflavus and Enterococcus flavescens. Antimicrob. Agents Chemother. 38:1788-1793.
50. Noble, C. J. 1978. Carriage of group D streptococci in the human bowel. J. Clin. Pathol. 31:1182-1186.
51. Ogier, J. C., andP. Serror. 2008. Safety assessment of dairy microorganisms: the Enterococcus genus. Int. J. Food Microbiol. 126:291-301.
52. Patel, R., J. R. Uhl, P. Kohner, M. K Hopkins, andF. R. Cockerill III. 1997. Multiplex PCR detection of vanA, vanB, vanC-1, and vanC-2/3 genes in enterococci. J. Clin. Microbiol. 35:703-707.
53. Poyart, C., G. Quesne, S. Coulon, P. Berche, andP. Trieu-Cuot. 1998. Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J. Clin. Microbiol. 36: 41-47.
54. Rajilic-Stojanovic, M., H. G. Heilig, D. Molenaar, K. Kajander, A. Surakka, H. Smidt, andW. M. de Vos. 2009. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ. Microbiol. 11:1736-1751.
55. Rinttila, T., A. Kassinen, E. Mahnen, L. Krogius, andA. Palva. 2004. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J. Appl. Microbiol. 97:1166-1177.
56. Ruimy, R., V. Breittmayer, V. Boivin, andR. Christen. 1994. Assessment of the state of activity of bacterial cells by hybridization with a RNA targeted fluorescently labelled oligonucleotidic probe. FEMS Microbiol. Ecol. 15: 207-214.
57. Ruoff, K. L., R. A. Whiley, and D. Beighton. 1998. Streptococcus, p. 283-296. In P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover, and R. H. Yolken (ed.), Manual of clinical microbiology, 7th ed. ASM Press, Washington, DC.
58. Sakaguchi, S., M. Saito, H. Tsuji, T. Asahara, O. Takata, J. Fujimura, S. Nagata, K Nomoto, andT. Shimizu. 2010. Bacterial ribosomal RNA-targeted reverse transcription PCR used to identify pathogens responsible for fever with neutropenia. J. Clin. Microbiol. 48:1624-1628.
59. Schleifer, K. H., andR. Kilpper-Bälz. 1987. Molecular and chemotaxonomic approaches to the classification of streptococci, enterococci and lactococci: a review. Syst. Appl. Microbiol. 10:1-19.
60. Schleifer, K. H., andR. 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.
61. Schleifer, K. H., J. Kraus, C. Dvorak, R. Kilpper-Bälz, M. D. Collins, and W. Fischer. 1985. Transfer of Streptococcus lactis and related Streptococci to the genus Lactococcus gen. nov. Syst. Appl. Microbiol. 6:183-195.
62. Schuchat, A. 1998. Epidemiology of group B streptococcal disease in the United States: shifting paradigms. Clin. Microbiol. Rev. 11:497-513.
63. Sghir, A., G. Gramet, A. Suau, V. Rochet, P. Pochart, andJ. Dore. 2000. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 66:2263-2266.
64. Sood, S., M. Malhotra, B. K. Das, andA. Kapil. 2008. Enterococcal infections and antimicrobial resistance. Indian J. Med. Res. 128:111-121.
65. Takada, T., K. Matsumoto, andK. Nomoto. 2004. Development of multicolor FISH method for analysis of seven Bifidobacterium species in human feces. J. Microbiol. Methods 58:413-421.
66. Toda, T., H. Kosaka, M. Terai, H. Mori, Y. Benno, andY. Yamori. 2005. Effects of fermented milk with Lactococcus lactis subsp. cremoris FC on defecation frequency and fecal microflora in healthy elderly volunteers. J. Jpn. Soc. Food Sci. Technol. 52:243-250.
67. Vanhaecke, L., F. Vercruysse, N. Boon, W. Verstraete, I. Cleenwerck, M. De Wachter, P. De Vos, and T. van de Wiele. 2008. Isolation and characterization of human intestinal bacteria capable of transforming the dietary carcinogen 2-amino-1-methyl-6-phenylimidazo[4.5-b]pyridine. Appl. Environ. Microbiol. 74:1469-1477.
68. Vendrell, D., J. L. Balcazar, I. Ruiz-Zarzuela, I. de Blas, O. Girones, andJ. L. Muzquiz. 2006. Lactococcus garvieae in fish: a review. Comp. Immunol. Microbiol. Infect. Dis. 29:177-198.
69. Wang, X., T. D. Allen, R. J. May, S. Lightfoot, C. W. Houchen, andM. M. Huycke. 2008. Enterococcus faecalis induces aneuploidy and tetraploidy in colonic epithelial cells through a bystander effect. Cancer Res. 68:9909-9917.
70. Woodmansey, E. J., M. E. McMurdo, G. T. Macfarlane, andS. Macfarlane. 2004. Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. Appl. Environ. Microbiol. 70:6113-6122.
71. Yano, A., N. Kaneko, H. Ida, T. Yamaguchi, andN. Hanada. 2002. Real-time PCR for quantification of Streptococcus mutans. FEMS Microbiol. Lett. 217:23-30.