Development of quantitative real-time PCR primers for detecting 42 oral bacterial species

Archives of Microbiology

Volumn 195, Issue 7, 2013, Pages 473-482

  Park, Soon Nang ^a   Lim, Yun Kyong ^a   Kook, Joong Ki ^a  

^a Chosun University   (South Korea)

Author keywords

Oral bacteria; Quantitative real time PCR primers; rpoB

Indexed keywords

GENOMIC DNA; RNA POLYMERASE BETA SUBUNIT;

ACTINOMYCES NAESLUNDII; AGGREGATIBACTER APHROPHILUS; ARTICLE; ATOPOBIUM RIMAE; BACTERIAL STRAIN; BACTERIUM; BACTERIUM DETECTION; CAMPYLOBACTER RECTUS; CAPNOCYTOPHAGA GINGIVALIS; CAPNOCYTOPHAGA OCHRACEA; CAPNOCYTOPHAGA SPUTIGENA; CONTROLLED STUDY; EIKENELLA CORRODENS; FUSOBACTERIUM NECROPHORUM; FUSOBACTERIUM NUCLEATUM; FUSOBACTERIUM PERIODONTICUM; FUSOBACTERIUM SIMIAE; LEPTOTRICHIA BUCCALIS; LIMIT OF DETECTION; MOUTH FLORA; NEISSERIA MENINGITIDIS; NEISSERIA SICCA; NEISSERIA SUBFLAVA; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PORPHYROMONAS ASACCHAROLYTICA; PORPHYROMONAS ENDODONTALIS; PREVOTELLA BARONIAE; PREVOTELLA BIVIA; PREVOTELLA BUCCAE; PREVOTELLA BUCCALIS; PREVOTELLA CORPORIS; PREVOTELLA DISIENS; PREVOTELLA INTERMEDIA; PREVOTELLA MARSHII; PREVOTELLA MELANINOGENICA; PREVOTELLA NIGRESCENS; PREVOTELLA ORALIS; PREVOTELLA ORIS; PREVOTELLA OULORUM; PREVOTELLA PALLENS; PREVOTELLA VERORALIS; PRIORITY JOURNAL; QUANTITATIVE REAL TIME POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; ROTHIA DENTOCARIOSA; RPOB GENE; SELENOMONAS NOXIA; SPECIES DIFFERENCE; STREPTOCOCCUS MUTANS; STREPTOCOCCUS ORALIS; STREPTOCOCCUS SANGUINIS; STREPTOCOCCUS SOBRINUS; TANNERELLA FORSYTHENSIS; TREPONEMA DENTICOLA; VEILLONELLA PARVULA;

BACTERIA; DNA PRIMERS; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; HUMANS; MOUTH; MOUTH DISEASES; POLYMERASE CHAIN REACTION; REAL-TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

ATOPOBIUM RIMAE; BACTERIA (MICROORGANISMS); FUSOBACTERIUM NUCLEATUM; NEISSERIA MENINGITIDIS; PORPHYROMONAS ASACCHAROLYTICA;

EID: 84879406251     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-013-0896-4     Document Type: Article

References (31)

1. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43:5721-5732
2. Abdeldaim GM, Strålin K, Korsgaard J, Blomberg J, Welinder-Olsson C, Herrmann B (2010) Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis. BMC Microbiol 10:310. doi: 10.1186/1471-2180-10-310
3. Aliyu SH, Marriott RK, Curran MD, Parmar S, Bentley N, Brown NM, Brazier JS, Ludlam H (2004) Real-time PCR investigation into the importance of Fusobacterium necrophorum as a cause of acute pharyngitis in general practice. J Med Microbiol 53:1029-1035
4. Ashimoto A, Chen C, Bakker I, Slots J (1996) Polymerase chain reaction detection of 8 putative periodontal pathogens in subgingival plaque of gingivitis and advanced periodontitis lesions. Oral Microbiol Immunol 11:266-273
5. Bizhang M, Ellerbrock B, Preza D, Raab W, Singh P, Beikler T, Henrich B, Zimmer S (2011) Detection of nine microorganisms from the initial carious root lesions using a TaqMan-based real-time PCR. Oral Dis 17:642-652. doi: 10.1111/j.1601-0825.2011.01815.x
6. Brito LC, Teles FR, Teles RP, França EC, Ribeiro-Sobrinho AP, Haffajee AD, Socransky SS (2007) Use of multiple-displacement amplification and checkerboard DNA-DNA hybridization to examine the microbiota of endodontic infections. J Clin Microbiol 45:3039-3049
7. Conrads G, Flemmig TF, Seyfarth I, Lampert F, Lutticken R (1999) Simultaneous detection of Bacteroides forsythus and Prevotella intermedia by 16S rRNA gene-directed multiplex PCR. J Clin Microbiol 37:1621-1624
8. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Fox AJ, Kaczmarski EB (2001) Simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in suspected cases of meningitis and septicemia using real-time PCR. J Clin Microbiol 39:1553-1558
9. Dolan Thomas J, Hatcher CP, Satterfield DA, Theodore MJ, Bach MC, Linscott KB, Zhao X, Wang X, Mair R, Schmink S, Arnold KE, Stephens DS, Harrison LH, Hollick RA, Andrade AL, Lamaro-Cardoso J, de Lemos AP, Gritzfeld J, Gordon S, Soysal A, Bakir M, Sharma D, Jain S, Satola SW, Messonnier NE, Mayer LW (2011) sodC-based real-time PCR for detection of Neisseria meningitidis. PLoS ONE 6:e19361. doi: 10.1371/journal.pone.0019361
10. Drancourt M, Raoult D (2002) rpoB gene sequence-based identification of Staphylococcus species. J Clin Microbiol 40:1333-1338
11. Haffajee AD, Bogren A, Hasturk H, Feres M, Lopez NJ, Socransky SS (2004) Subgingival microbiota of chronic periodontitis subjects from different geographic locations. J Clin Periodontol 31:996-1002
12. Hyvärinen K, Laitinen S, Paju S, Hakala A, Suominen-Taipale L, Skurnik M, Könönen E, Pussinen PJ (2009) Detection and quantification of five major periodontal pathogens by single copy gene-based real-time PCR. Innate Immun 15:195-204. doi: 10.1177/1753425908101920
13. Jensen A, Hagelskjaer Kristensen L, Prag J (2007) Detection of Fusobacterium necrophorum subsp. funduliforme in tonsillitis in young adults by real-time PCR. Clin Microbiol Infect 13:695-701
14. Kato H, Yoshida A, Awano S, Ansai T, Takehara T (2005) Quantitative detection of volatile sulfur compound- producing microorganisms in oral specimens using real-time PCR. Oral Dis 11:67-71 Erratum in: Oral Dis 2005;15:120
15. Khamis A, Raoult D, La Scola B (2004) rpoB gene sequencing for identification of Corynebacterium species. J Clin Microbiol 42:3925-3931
16. Kim HS, Lee DS, Chang YH, Kim MJ, Koh S, Kim J, Seong JH, Song SK, Shin HS, Son JB, Jung MY, Park SN, Yoo SY, Cho KW, Kim DK, Moon S, Kim D, Choi Y, Kim BO, Jang HS, Kim CS, Kim C, Choe SJ, Kook JK (2010) Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies. J Clin Microbiol 48:545-553. doi: 10.1128/JCM.01631-09
17. Kozarov E, Sweier D, Shelburne C, Progulske-Fox A, Lopatin D (2006) Detection of bacterial DNA in atheromatous plaques by quantitative PCR. Microbes Infect 8:687-693
18. Krieg NR (2001) Identification of prokaryotes. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology, vol 1, 2nd edn. Springer-Verlag, New York, pp 33-38
19. Kuboniwa M, Amano A, Kimura KR, Sekine S, Kato S, Yamamoto Y, Okahashi N, Iida T, Shizukuishi S (2004) Quantitative detection of periodontal pathogens using real-time polymerase chain reaction with TaqMan probes. Oral Microbiol Immunol 19:168-176
20. Kumar PS, Griffen AL, Barton JA, Paster BJ, Moeschberger ML, Leys EJ (2003) New bacterial species associated with chronic periodontitis. J Dent Res 82:338-344
21. Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, Arai H, Tanimoto I, Nishimura F, Takashiba S (2003) Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol 39:81-86
22. Nonnenmacher C, Dalpke A, Mutters R, Heeg K (2004) Quantitative detection of periodontopathogens by real-time PCR. J Microbiol Methods 59:117-125
23. Nonnenmacher C, Dalpke A, Rochon J, Flores-de-Jacoby L, Mutters R, Heeg K (2005) Real-time polymerase chain reaction for detection and quantification of bacteria in periodontal patients. J Periodontol 76:1542-1549
24. Park SN, Park JY, Kook JK (2011) Development of Porphyromonas gingivalis-specific quantitative real-time PCR primers based on the nucleotide sequence of rpoB. J Microbiol 49:315-319. doi: 10.1007/s12275-011-1028-y
25. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, Sahasrabudhe A, Dewhirst FE (2001) Bacterial diversity in human subgingival plaque. J Bacteriol 183:3770-3783
26. Price RR, Viscount HB, Stanley MC, Leung KP (2007) Targeted profiling of oral bacteria in human saliva and in vitro biofilms with quantitative real-time PCR. Biofouling 23:203-213
27. Saito D, Coutinho LL, Borges Saito CP, Tsai SM, Höfling JF, Gonçalves RB (2009) Real-time polymerase chain reaction quantification of Porphyromonas gingivalis and Tannerella forsythia in primary endodontic infections. J Endod 35:1518-1524. doi: 10.1016/j.joen.2009.08.005
28. Saygun I, Kubar A, Sahin S, Sener K, Slots J (2008) Quantitative analysis of association between herpesviruses and bacterial pathogens in periodontitis. J Periodontal Res 43:352-359
29. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A (1996) Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. J Biol Chem 271:27969-27974
30. Yoo SY, Kim KJ, Lim SH, Kim KW, Hwang HK, Min BM, Choe SJ, Kook JK (2005) First isolation of Streptococcus downei from human dental plaques. FEMS Microbiol Lett 249:323-326
31. Yoshida A, Suzuki N, Nakano Y, Kawada M, Oho T, Koga T (2003) Development of a 5′nuclease-based real-time PCR assay for quantitative detection of cariogenic dental pathogens Streptococcus mutans and Streptococcus sobrinus. J Clin Microbiol 41:4438-4441