Diagnostic accuracy of a 16S ribosomal DNA gene-based molecular technique (RT-PCR, microarray, and sequencing) for bacterial meningitis, early-onset neonatal sepsis, and spontaneous bacterial peritonitis

Diagnostic Microbiology and Infectious Disease

Volumn 69, Issue 2, 2011, Pages 153-160

  Esparcia, Oscar ^a,b   Montemayor, Michel ^a   Ginovart, Gemma ^a   Pomar, Virginia ^a   Soriano, Germán ^a,d   Pericas, Roser ^a   Gurgui, Mercedes ^a   Sulleiro, Elena ^c   Prats, Guillem ^b,c   Navarro, Ferran ^a,b   Coll, Pere ^a,b  

^a HOSPITAL DE LA SANTA CREU I SANT PAU   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^d INSTITUTO DE SALUD CARLOS III   (Spain)

Author keywords

16S rDNA; Bacterial detection; Molecular biology; Theranostics

Indexed keywords

BACTERIAL DNA; DNA 16S;

ARTICLE; BACTERIAL MENINGITIS; BACTERIAL PERITONITIS; BACTERIUM CULTURE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA DETERMINATION; DNA MICROARRAY; DNA SEQUENCE; EARLY ONSET NEONATAL SEPSIS; HUMAN; INTERMETHOD COMPARISON; MOLECULAR BIOLOGY; NEWBORN SEPSIS; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SPONTANEOUS BACTERIAL PERITONITIS;

BACTERIA; BACTERIAL INFECTIONS; HUMANS; INFANT, NEWBORN; MENINGITIS, BACTERIAL; MOLECULAR DIAGNOSTIC TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PERITONITIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEPSIS; SEQUENCE ANALYSIS, DNA;

EID: 78651466515     PISSN: 07328893     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2010.10.022     Document Type: Article

References (43)

1. Aragón L.M., Navarro F., Heiser V., Garrigó M., Español M., Coll P. Rapid detection of specific gene mutations associated with isoniazid or rifampicin resistance in Mycobacterium tuberculosis clinical isolates using non-fluorescent low-density DNA microarrays. J. Antimicrob. Chemother. 2006, 57:825-831.
2. Brozanski B.S., Jones J.G., Krohn M.J., Jordan J.A. Use of polymerase chain reaction as a diagnostic tool for neonatal sepsis can result in a decrease in use of antibiotics and total neonatal intensive care unit length of stay. J. Perinatol. 2006, 26:688-692.
3. Carroll N.M., Adamson P., Okhravi N. Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion. J. Clin. Microbiol. 1999, 37:3402-3404.
4. Corless C.E., Guiver M., Borrow R., Edwards-Jones V., Fox A.J., Kaczmarski E.B. Simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in suspected cases of meningitis and septicemia using real-time PCR. J. Clin. Microbiol. 2001, 39:1553-1558.
5. Corless C.E., Guiver M., Borrow R., Edwards-Jones V., Kaczmarski E.B., Fox A.J. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol. 2000, 38:1747-1752.
6. Deutch S., Pedersen L.N., Podenphant L., Olesen R., Schmidt M.B., Moller J.K., Ostergaard L. Broad-range real time PCR and DNA sequencing for the diagnosis of bacterial meningitis. Scand. J. Infect. Dis. 2006, 38:27-35.
7. Dicuonzo G., Lorino G., Lilli D., Rivanera D., Guarino P., Angeletti S., Gherardi G., Candida S., Filadoro F. Use of oligoprobes on amplified DNA in the diagnosis of bacterial meningitis. Eur. J. Clin. Microbiol. Infect. Dis. 1999, 18:352-357.
8. Francés R., Benlloch S., Zapater P., González J.M., Lozano B., Muñoz C., Pascual S., Casellas J.A., Uceda F., Palazón J.M., Carnicer F., Pérez-Mateo M., Such J. A sequential study of serum bacterial DNA in patients with advanced cirrhosis and ascites. Hepatology 2004, 39:484-491.
9. Frances R., Zapater P., Gonzalez-Navajas J.M., Munoz C., Cano R., Moreu R., Pascual S., Bellot P., Perez-Mateo M., Such J. Bacterial DNA in patients with cirrhosis and noninfected ascites mimics the soluble immune response established in patients with spontaneous bacterial peritonitis. Hepatology 2008, 47:978-985.
10. Frothingham R., Blitchington R.B., Lee D.H., Greene R.C., Wilson K.H. UV absorption complicates PCR decontamination. Biotechniques 1992, 13:208-210.
11. Gerdes J.S. Clinicopathologic approach to the diagnosis of neonatal sepsis. Clin. Perinatol. 1991, 18:361-381.
12. Guiver M., Borrow R., Marsh J., Gray S.J., Kaczmarski E.B., Howells D., Boseley P., Fox A.J. Evaluation of the Applied Biosystems automated Taqman polymerase chain reaction system for the detection of meningococcal DNA. FEMS. Immunol. Med. Microbiol. 2000, 28:173-179.
13. Heininger A., Binder M., Ellinger A., Botzenhart K., Unertl K., Doring G. DNase pretreatment of master mix reagents improves the validity of universal 16S rRNA gene PCR results. J. Clin. Microbiol. 2003, 41:1763-1765.
14. Heininger A., Binder M., Ellinger A., Pfisterer J., Botzenhart K., Unertl K., Doering G. Effect of comprehensive validation of the template isolation procedure on the reliability of bacteraemia detection by a 16S rRNA gene PCR. Clin. Microbiol. Infect. 2004, 10:452-458.
15. Hilali F., Saulnier P., Chachaty E., Andremont A. Decontamination of polymerase chain reaction reagents for detection of low concentrations of 16S rRNA genes. Mol. Biotechnol. 1997, 7:207-216.
16. Jordan J.A., Durso M.B. Comparison of 16S rRNA Gene PCR and BACTEC 9240 for detection of neonatal bacteremia. J. Clin. Microbiol. 2000, 38:2574-2578.
17. Jordan J.A., Durso M.B. Real-time polymerase chain reaction for detecting bacterial DNA directly from blood of neonates being evaluated for sepsis. J. Mol. Diagn. 2005, 7:575-581.
18. Jordan J.A., Durso M.B., Butchko A.R., Jones J.G., Brozanski B.S. Evaluating the near-term infant for early onset sepsis: progress and challenges to consider with 16S rDNA polymerase chain reaction testing. J. Mol. Diagn. 2006, 8:357-363.
19. Kellogg J.A., Ferrentino F.L., Goodstein M.H., Liss J., Shapiro S.L., Bankert D.A. Frequency of low level bacteremia in infants from birth to two months of age. Pediatr. Infect. Dis. J. 1997, 16:381-385.
20. Kotilainen P., Jalava J., Meurman O., Lehtonen O.P., Rintala E., Seppala O.P., Eerola E., Nikkari S. Diagnosis of meningococcal meningitis by broad-range bacterial PCR with cerebrospinal fluid. J. Clin. Microbiol. 1998, 36:2205-2209.
21. Laforgia N., Coppola B., Carbone R., Grassi A., Mautone A., Iolascon A. Rapid detection of neonatal sepsis using polymerase chain reaction. Acta. Paediatr. 1997, 86:1097-1099.
22. Lane D. 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics 1991, John Wiley, Chischester. E. Stackebrandt, M. Goodfellow (Eds.).
23. Lu J.J., Perng C.L., Lee S.Y., Wan C.C. Use of PCR with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid. J. Clin. Microbiol. 2000, 38:2076-2080.
24. Margall N., Majó M., Latorre C., Fontanals D., Domínguez A., Prats G. Use of universal PCR on cerebrospinal fluid to diagnose bacterial meningitis in culture-negative patients. Eur. J. Clin. Microbiol. Infect. Dis. 2002, 21:67-69.
25. McCabe K.M., Khan G., Zhang Y.H., Mason E.O., McCabe E.R. Amplification of bacterial DNA using highly conserved sequences: automated analysis and potential for molecular triage of sepsis. Pediatrics 1995, 95:165-169.
26. Millar B.C., Xu J., Moore J.E. Risk assessment models and contamination management: implications for broad-range ribosomal DNA PCR as a diagnostic tool in medical bacteriology. J Clin Microbiol 2002, 40:1575-1580.
27. Ortiz J., Soriano G., Coll P., Novella M.T., Pericas R., Sabat M., Sánchez F., Guarner C., Prats G., Vilardell F. Early microbiologic diagnosis of spontaneous bacterial peritonitis with BacT/ALERT. J. Hepatol. 1997, 26:839-844.
28. Picard F.J., Bergeron M.G. Rapid molecular theranostics in infectious diseases. Drug. Discov. Today. 2002, 7:1092-1101.
29. Rantakokko-Jalava K., Nikkari S., Jalava J., Eerola E., Skurnik M., Meurman O., Ruuskanen O., Alanen A., Kotilainen E., Toivanen P., Kotilainen P. Direct amplification of rRNA genes in diagnosis of bacterial infections. J. Clin. Microbiol. 2000, 38:32-39.
30. Rochelle P.A., Weightman A.J., Fry J.C. DNase I treatment of Taq DNA polymerase for complete PCR decontamination. Biotechniques 1992, 13:520.
31. Saravolatz L.D., Manzor O., VanderVelde N., Pawlak J., Belian B. Broad-range bacterial polymerase chain reaction for early detection of bacterial meningitis. Clin. Infect. Dis. 2003, 36:40-45.
32. Soriano G., Esparcia O., Montemayor M., Guarner-Argente C., Pericas R., Torras T., Calvo N., Román E., Navarro F., Guarner C., Coll P. Bacterial DNA in the diagnosis of spontaneous bacterial peritonitis. Aliment. Pharmacol. Ther. 2011, 33:275-284.
33. Schrag S.J., Zell E.R., Lynfield R., Roome A., Arnold K.E., Craig A.S., Harrison L.H., Reingold A., Stefonek K., Smith G., Gamble M., Schuchat A. A population-based comparison of strategies to prevent early-onset group B streptococcal disease in neonates. N. Engl. J. Med. 2002, 347:233-239.
34. Schuurman T., de Boer R.F., Kooistra-Smid A.M., van Zwet A.A. 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. J. Clin. Microbiol. 2004, 42:734-740.
35. Shang S., Chen G., Wu Y., Du L., Zhao Z. Rapid diagnosis of bacterial sepsis with PCR amplification and microarray hybridization in 16S rRNA gene. Pediatr. Res. 2005, 58:143-148.
36. Shang S., Chen Z., Yu X. Detection of bacterial DNA by PCR and reverse hybridization in the 16S rRNA gene with particular reference to neonatal septicemia. Acta. Paediatr. 2001, 90:179-183.
37. Sharma J.K., Gopalkrishna V., Das B.C. A simple method for elimination of unspecific amplifications in polymerase chain reaction. Nucleic Acids Res. 1992, 20:6117-6118.
38. Such J., Francés R., Muñoz C., Zapater P., Casellas J.A., Cifuentes A., Rodríguez-Valera F., Pascual S., Sola-Vera J., Carnicer F., Uceda F., Palazón J.M., Pérez-Mateo M. Detection and identification of bacterial DNA in patients with cirrhosis and culture-negative, nonneutrocytic ascites. Hepatology 2002, 36:135-141.
39. Sugihara T., Koda M., Maeda Y., Matono T., Nagahara T., Mandai M., Ueki M., Murawaki Y. Rapid identification of bacterial species with bacterial DNA microarray in cirrhotic patients with spontaneous bacterial peritonitis. Intern. Med. 2009, 48:3-10.
40. Vieira S.M., da Silveira T.R., Matte U., Kieling C.O., Ferreira C.T., Taniguchi A., Oliveira Fdos S., Barth A.L. Amplification of bacterial DNA does not distinguish patients with ascitic fluid infection from those colonized by bacteria. J. Pediatr. Gastroenterol. Nutr. 2007, 44:603-607.
41. Wiest R., Garcia-Tsao G. Bacterial translocation (BT) in cirrhosis. Hepatology 2005, 41:422-433.
42. Zapater P., Francés R., González-Navajas J.M., de la Hoz M.A., Moreu R., Pascual S., Monfort D., Montoliu S., Vila C., Escudero A., Torras X., Cirera I., Llanos L., Guarner-Argente C., Palazón J.M., Carnicer F., Bellot P., Guarner C., Planas R., Solá R., Serra M.A., Munoz C., Pérez-Mateo M., Such J. Serum and ascitic fluid bacterial DNA: a new independent prognostic factor in noninfected patients with cirrhosis. Hepatology 2008, 48:1924-1931.
43. Zucol F., Ammann R.A., Berger C., Aebi C., Altwegg M., Niggli F.K., Nadal D. Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification. J. Clin. Microbiol. 2006, 44:2750-2759.