Prospective Study of Use of PCR Amplification and Sequencing of 16S Ribosomal DNA from Cerebrospinal Fluid for Diagnosis of Bacterial Meningitis in a Clinical Setting

Journal of Clinical Microbiology

Volumn 42, Issue 2, 2004, Pages 734-740

  Schuurman, Tim ^a   De Boer, Richard F ^a   Kooistra Smid, Anna M D ^a   Van Zwet, Anton A ^a  

^a Public Health Service of Groningen   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S;

ADOLESCENT; ADULT; AGED; ARTICLE; BACTERIAL MENINGITIS; CEREBROSPINAL FLUID ANALYSIS; CHILD; DIAGNOSTIC ACCURACY; ESCHERICHIA COLI; FEMALE; FUSOBACTERIUM NUCLEATUM; HAEMOPHILUS INFLUENZAE; HUMAN; INFANT; LISTERIA MONOCYTOGENES; MAJOR CLINICAL STUDY; MALE; NEISSERIA MENINGITIDIS; NEWBORN; NUCLEOTIDE SEQUENCE; PANTOEA; POLYMERASE CHAIN REACTION; PREVOTELLA BIVIA; PRIORITY JOURNAL; RNA ANALYSIS; RNA GENE; RNA SEQUENCE; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS SALIVARIUS;

BASE SEQUENCE; DNA PRIMERS; DNA, RIBOSOMAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; GENE AMPLIFICATION; HUMANS; MENINGITIS, BACTERIAL; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; STAPHYLOCOCCAL INFECTIONS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FUSOBACTERIUM; FUSOBACTERIUM NUCLEATUM; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; LISTERIA; LISTERIA MONOCYTOGENES; NEGIBACTERIA; NEISSERIA; NEISSERIA MENINGITIDIS; PANTOEA; POSIBACTERIA; PREVOTELLA; PREVOTELLA BIVIA; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS SALIVARIUS;

EID: 1242336853     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.2.734-740.2004     Document Type: Article

References (61)

1. Akhaddar, A., B. El Mostarchid, M. Gazzaz, and M. Boucetta. 2002. Cerebellar abscess due to Lactococcus lactis: a new pathogen. Acta Neurochir. 144:305-306.
2. Bäckman, A., P. G. Lantz, P. Rädström, and P. Olcén. 1999. Evaluation of an extended diagnostic PCR assay for detection and verification of the common causes of bacterial meningitis in CSF and other biological samples. Mol. Cel. Probes 13:49-60.
3. Boom, R., C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:495-503.
4. Boom, R., C. J. A. Sol, T. Schuurman, A. van Breda, J. F. L. Weel, M. Beld, I. J. M. ten Berge, P. M. E. Wertheim-van Dillen, and M. D. de Jong. 2002. Human cytomegalovirus DNA in plasma and serum specimens of renal transplant recipients is highly fragmented. J. Clin. Microbiol. 40:4105-4113.
5. Böttger, E. C. 1989. Rapid determination of bacterial rRNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol. Lett. 53:171-176.
6. Böttger, E. C. 1990. Frequent contamination of Taq polymerase with DNA. Clin. Chem. 36:1258-1259.
7. Brisson-Noël, A., C. Aznar, C. Chureau, S. Nguyen, C. Pierre, M. Bartoli, R. Bonete, G. Pialoux, B. Gicquel, and G. Garrique. 1991. Diagnosis of tuberculosis by DNA amplification in clinical practice evaluation. Lancet 338:364-366.
8. Busch, N., P. R. Mertens, T. Schonfelder, H. Nguyen, H. U. Marschall, H. Kierdorf, G. Haase, R. Urhahn, H. G. Sieberth, and S. Matern. 1996. Lemierre's post-tonsillitis sepsis with meningitis and intravascular consumption coagulopathy as complication of infectious mononucleosis with pansinusitis. Dtsch. Med. Wochenschr. 121:94-98.
9. Carroll, N. M., P. Adamson, and N. Okhravi. 1999. Elimination of bacterial DNA from TaqDNA polymerases by restriction endonuclease digestion. J. Clin. Microbiol. 37:3402-3404.
10. Cherian, T., M. K. Lalitha, A. Manoharan, K. Thomas, R. H. Yolken, and M. C. Steinhoff. 1998. PCR-enzyme immunoassay for detection of Streptococcus pneumoniae DNA in cerebrospinal fluid samples from patients with culture-negative meningitis. J. Clin. Microbiol. 36:3605-3608.
11. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-11): previewing a new autoaligner that allows regular updates and the new prokaryotic taxynomy. Nucleic Acids Res. 31:442-443.
12. Corless, C. E., M. Guiver, R. Borrow, V. Edwards-Jones, A. J. Fox, and E. B. Kaczmarski. 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.
13. Corless, C. E., M. Guiver, R. Borrow, V. Edwards-Jones, E. B. Kaczmarski, and A. J. Fox. 2000. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol. 38:1747-1752.
14. Dicuonzo, G., G. Lorino, D. Lilli, D. Rivanera, P. Guarino, S. Angeletti, G. Gherardi, and F. Filadoro. 1999. Polymerase chain reaction, with sequencing, as a diagnostic tool in culture-negative bacterial meningitis. Clin. Microbiol. Infect. 5:92-96.
15. Dorigo-Zetsma, J. W., R. P. Verkooyen, H. P. van Helden, H. van der Nat, and J. M. van den Bosch. 2001. Molecular detection of Mycoplasma pneumoniae in adults with community-acquired pneumonia requiring hospitalization. J. Clin. Microbiol. 39:1184-1186.
16. Durand, M. L., S. B. Calderwood, D. J. Weber, S. I. Miller, F. S. Southwick, V. S. Caviness, Jr., and M. N. Schwartz. 1993. Acute bacterial meningitis in adults: a review of 493 episodes. N. Engl. J. Med. 328:21-28.
17. Durand, J. M., M. C. Rousseau, J. M. Gandois, G. Kaplanski, M. N. Mallet, and J. Soubeyrand. 1995. Streptococcus lactis septicemia in a patient with chronic lymphocytic leukemia. Am. J. Hematol. 50:64-65.
18. Dyer, J. R., B. L. Gilliam, J. J. Eron, Jr., L. Grosso, M. S. Cohen, and S. A. Fiscus. 1996. Quantitation of human immunodeficiency virus type 1 RNA in cell free seminal plasma: comparison of NASBA™ with Amplicor™ reverse transcription-PCR amplification and correlation with quantitative culture. J. Virol. Methods 60:161-170.
19. Facklam, R., and J. A. Elliott. 1995. Identification, classification and clinical relevance of catalase-negative, gram-positive cocci, excluding the streptococci and enterococci. Clin. Microbiol. Rev. 8:479-495.
20. Fidler, H. M., G. A. Rook, N. M. Johnson, and J. McFadden. 1993. Mycobacterium tuberculosis DNA in tissue affected by sarcoidosis. BMJ 306:546-549.
21. Frothingham, R., R. B. Blitchington, D. H. Lee, R. C. Greene, and K. H. Wilson. 1992. UV absorption complicates PCR decontamination. BioTechniques 13:208-210.
22. Hall, L. M. C., B. Duke, and G. Urwin. 1995. An approach to the identification of the pathogens of bacterial meningitis by the polymerase chain reaction. Eur. J. Clin. Microbiol. Infect. Dis. 14:1090-1094.
23. Hale, A. D., J. Green, and D. W. G. Brown. 1996. Comparison of four RNA extraction methods for the detection of small round viruses in faecal specimens. J. Virol. Methods 57:195-201.
24. Hand, O., M. Höss, M. Krings, and S. Pääbo. 1994. Ancient DNA: methodological challenges. Experientia 50:524-529.
25. Heininger, A., M. Binder, A. Ellinger, K. Botzenhart, K. Unertl, and G. Döring. 2003. DNase pretreatment of master mix reagents improves the validity of universal 16S rRNA gene PCR results. J. Clin. Microbiol. 41: 1763-1765.
26. Hilali, F., P. Saulnier, F. Chachaty, and A. Andremont. 1997. Decontamination of polymerase chain reaction reagents for detection of low concentration of 16S rRNA genes. Mol. Biotechnol. 7:207-216.
27. Hughes, M. S., L. A. Beck, and R. A. Skuce. 1994. Identification and elimination of DNA sequences in TaqDNA polymerase. J. Clin. Microbiol. 32: 2007-2008.
28. Jinno, Y., K. Yoshiura, and N. Niikawa. 1990. Use of psoralen as extinguisher of contaminating DNA in PCR. Nucleic Acids Res. 18:6739.
29. Kirschner, P., J. Rosenau, B. Springer, K. Teschner, K. Feldmann, and E. C. Böttger. 1996. Diagnosis of mycobacterial infections by nucleic acid amplification: 18-month prospective study. J. Clin. Microbiol. 34:304-312.
30. Kotilainen, P., J. Jalava, O. Meurman, O. Lehtonen, E. Rintala, O. Seppälä, E. Eerola, and S. Nikkari. 1998. Diagnosis of meningococcal meningitis by broad-range bacterial PCR with cerebrospinal fluid. J. Clin. Microbiol. 36: 2205-2209.
31. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley & Sons, Chichester, United Kingdom.
32. La Scolea, L. J., Jr., and D. Dryja. 1984. Quantitation of bacteria in cerebrospinal fluid and blood of children with meningitis and its diagnostic significance. J. Clin. Microbiol. 19:187-190.
33. Lu, J.-J., C.-L. Perng, S.-Y. Lee, and C.-C. Wan. 2000. Use of PCR with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid. J. Clin. Microbiol. 38:2076-2080.
34. Mahony, J. B., X. Song, S. Chong, M. Faught, T. Salonga, and J. Kapala. 2001. Evaluation of the NucliSens basic kit for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in genital tract specimens using nucleic acid sequence-based amplification of 16S rRNA. J. Clin. Microbiol. 39:1429-1435.
35. Margall Coscojuela, N., M. Majó Moreno, C. Latorre Otín, D. Fontanals Aymerich, À. Domínquez García, and G. Prats Pastor. 2002. Use of universal PCR on cerebrospinal fluid to diagnose bacterial meningitis in culture-negative patients. Eur. J. Clin. Microbiol. Infect. Dis. 21:67-69.
36. Millar, B. C., J. Xu, and J. E. Moore. 2002. Risk assessment models and contamination management: implications for broad-range ribosomal DNA PCR as a diagnostic tool in medical bacteriology. J. Clin. Microbiol. 40:1575-1580.
37. Nakarai, T., K. Morita, Y. Nojiri, J. Nei, and Y. Kawamori. 2000. Liver abscess due to Lactococcus lactis cremoris. Pediatr. Int. 42:699-701.
38. Nijhuis, M., N. van Maarseveen, R. Schuurman, S. Verkuijlen, M. de Vos, K. Hendriksen, and A. M. van Loon. 2002. Rapid and sensitive routine detection of all members of the genus Enterovirus in different clinical specimens by real-time PCR. J. Clin. Microbiol. 40:3666-3670.
39. Nikkari, S., F. A. Lopez, P. W. Lepp, P. R. Cieslak, S. Ladd-Wilson, D. Passaro, R. Danila, and D. A. Relman. 2002. Broad-range bacterial detection and the analysis of unexplained death and critical illness. Emerg. Infect. Dis. 8:188-193.
40. Rand, K. H., and H. Houck. 1990. Taq polymerase contains bacterial DNA of unknown origin. Mol. Cell. Probes 4:445-450.
41. Rantakokko-Jalava, K., and J. Jalava. 2002. Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR. J. Clin. Microbiol. 40:4211-4217.
42. Rantakokko-Jalava, K., S. Nikkari, J. Jalava, E. Eerola, M. Skurnik, O. Meurman, O. Ruuskanen, A. Alanen, E. Kotilainen, P. Toivanen, and P. Kotilainen. 2000. Direct amplification of rRNA genes in diagnosis of bacterial infections. J. Clin. Microbiol. 38:32-39.
43. Revello, M. G., F. Baldanti, A. Sarasini, M. Zavattoni, M. Torsellini, and G. Gerna. 1997. Prenatal diagnosis of rubella virus infection by direct detection and semiquantitation of viral RNA in clinical samples by reverse transcriptase-PCR. J. Clin. Microbiol. 35:708-713.
44. Rochelle, P. A., A. J. Weightman, and J. C. Fry. 1992. DNase 1 treatment of TaqDNA polymerase for complete PCR decontamination. BioTechniques 13:520.
45. Saravolatz, L. D., O. Manzor, N. VanderVelde, J. Pawlak, and B. Belian. 2003. Broad-range bacterial polymerase chain reaction for early detection of bacterial meningitis. Clin. Infect. Dis. 36:40-45.
46. Saunders, N. B., D. R. Shoemaker, B. L. Brandt, and W. D. Zollinger. 1997. Confirmation of suspicious cases of meningococcal meningitis by PCR and enzyme-linked immunosorbent assay. J. Clin. Microbiol. 35:3215-3219.
47. Schmidt, T. M., B. Pace, and N. R. Pace. 1991. Detection of DNA contamination in Taq polymerase. BioTechniques 11:176-177.
48. Schee, C. van der, A. van Belkum, L. Zwijers, E. van der Brugge, E. L. O'neill, A. A. Luijendijk, T. van Rijsoort-Vos, W. I. van der Meijden, H. Verbrugh, and H. J. F. Sluiters. 1999. Improved diagnosis of Trichomonas vaginalis infection by PCR using vaginal swabs and urine specimens compared to diagnosis by wet mount microscopy, culture, and fluorescent staining. J. Clin. Microbiol. 37:4127-4130.
49. Schoone, G. J., L. Oskam, N. C. M. Kroon, H. D. F. H. Schallig, and S. A. Omar. 2000. Detection and quantification of Plasmodium falciparum in blood samples using quantitative nucleic acid sequence-based amplification. J. Clin. Microbiol. 38:4040-4072.
50. Secchiero, P., D. R. Carrigan, Y. Asano, L. Benedetti, R. W. Crowley, A. L. Komaroff, R. C. Gallo, and P. Lusso. 1995. Detection of human herpesvirus 6 in plasma of children with primary infection and immunosuppressed patients by polymerase chain reaction. J. Infect. Dis. 171:273-280.
51. Seward, R. J., and K. J. Towner. 2000. Use of an automated DNA analysis system (DARAS®) for sequence-specific recognition of Neisseria meningitidis DNA. Clin. Microbiol. Infect. 6:29-33.
52. Sharma, J. K., V. Gopalkrishna, and B. C. Das. 1992. A simple method for elimination of unspecific amplifications in polymerase chain reaction. Nucleic Acids Res. 20:6117-6118.
53. Solmone, M., E. Girardi, F. Costa, L. Pucillo, G. Ippolito, and M. R. Capobianchi. 2002. Simple and reliable method for detection and genotyping of hepatitis C virus RNA in dried blood spots stored at room temperature. J. Clin. Microbiol. 40:3512-3514.
54. Taha, M.-K. 2000. Simultaneous approach for nonculture PCR-based identification and serogroup prediction of Neisseria meningitidis. Clin. Microbiol. 38:855-857.
55. Tunkel, A. R., and W. M. Scheld. 1995. Acute bacterial meningitis. Lancet 346:1675-1680.
56. Vernazza, P. L., J. R. Dyer, S. A. Fiscus, J. J. Eron, and M. S. Cohen. 1997. HIV-1 viral load in blood, semen and saliva. AIDS 11:1058-1059.
57. Wall, S., Z. M. Kunze, S. Saboor, J. Soufleri, P. Seechurn, R. Chiodini, and J. J. McFadden. 1993. Identification of sheroplast-like agents isolated from tissues of patients with Crohn's disease and control tissues by polymerase chain reaction. J. Clin. Microbiol. 31:1241-1245.
58. Wilson, K., R. Blitchington, and R. Greene. 1990. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28:1942-1946.
59. Wood, H. F., K. Jacobs, and M. McCarthy. 1985. Streptococcus lactis isolated from a patient with subacute bacterial endocarditis. Am. J. Med. 18:345-347.
60. Xu, J., B. C. Millar, J. E. Moore, K. Murphy, H. Webb, A. J. Fox, M. Cafferkey, and M. J. Crowe. 2003. Employment of broad-range 16S rRNA PCR to detect etiological agents of infection from clinical specimens in patients with acute meningitis: rapid separation of 16S rRNA PCR amplicons without the need for cloning. J. Appl. Microbiol. 94:197-206.
61. Zipeto, D., F. Baldanti, D. Zella, M. Furione, A. Cavicchini, G. Milanesi, and G. Gerna. 1993. Quantification of human cytomegalovirus DNA in peripheral blood polymorphonuclear leukocytes of immunocompromised patients by the polymerase chain reaction. J. Virol. Methods 44:45-46.