Toward rapid real-time molecular diagnostic to guide smart use of antimicrobials

Current Opinion in Microbiology

Volumn 5, Issue 5, 2002, Pages 478-482

  Boissinot, Maurice ^a,b   Bergeron, Michel G ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; ANTIINFECTIVE AGENT; BACTERIAL DNA; DNA; ISONIAZID; NUCLEIC ACID; PROTEIN; RIFAMPICIN; VANCOMYCIN;

ANTIBIOTIC RESISTANCE; ASSAY; DATA BASE; GENOME; GENOTYPE; HYBRIDIZATION; MUTATION; POLYMERASE CHAIN REACTION; REVIEW;

BACTERIA (MICROORGANISMS);

EID: 0036792158     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(02)00362-4     Document Type: Review

References (48)

1. Woods GL, Walker DH: Detection of infection or infectious agents by use of cytologic and histologic stains. Clin Microbiol Rev 1996, 9:382-404.
2. Procop GW, Wilson M: Infectious disease pathology. Clin Infect Dis 2001, 32:1589-1601.
3. Owens S: Killing the right bug. Phenotypic and genotypic approaches for identifying infectious agents and antibiotic resistance can help to slow the increasing antibiotic resistance among infectious bacteria. EMBO Rep 2001, 2:757-760.
4. Bergeron MG, Ouellette M: Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory. J Clin Microbiol 1998, 36:2169-2172.
5. Bergeron MG: Rapid polymerase chain reaction detection of bacteria and their antibiotic resistance genes: improved management, better treatment, and less resistance. Curr Infect Dis Rep 2001, 3:201-202.
6. Schweitzer B, Kingsmore S: Combining nucleic acid amplification and detection. Curr Opin Biotechnol 2001, 12:21-27.
7. Cloud JL, Neal H, Rosenberry R, Turenne CY, Jama M, Hillyard DR, Carroll KC: Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol 2002, 40:400-406.
8. Asai T, Zaporojets D, Squires C, Squires CL: An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci USA 1999, 96:1971-1976
9. CDC: Staphylococcus aureus resistant to vancomycin - United States, 2002. MMWR Morb Mortal Wkly Rep 2002, 51:565-567.
10. Garcia de Viedma D, del Sol Diaz Infantes M, Lasala F, Chaves F, Alcala L, Bouza E: New real-time PCR able to detect in a single tube multiple rifampin resistance mutations and high-level isoniazid resistance mutations in Mycobacterium tuberculosis. J Clin Microbiol 2002, 40:988-995.
11. Jungkind D, Kessler HH: Molecular methods for diagnosis of infectious diseases. In Manual of Commercial Methods in Clinical Microbiology. Edited by Truant AL. ASM Press; 2002:306-323.
12. Ke D, Ménard C, Picard FJ, Boissinot M, Ouellette M, Roy PH, Bergeron MG: Development of conventional and real-time PCR assays for the rapid detection of group B streptococci. Clin Chem 2000, 46:324-331.
13. Bélanger SD, Boissinot M, Menard C, Picard FJ, Bergeron MG: Rapid detection of Shiga toxin-producing bacteria in feces by multiplex PCR with molecular beacons on the Smart Cycler. J Clin Microbiol 2002, 40:1436-1440.
14. Anderson RC, Su X, Bogdan GJ, Fenton J: A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res 2000, 28:E60
15. Yuen PK, Kricka LJ, Fortina P, Panaro NJ, Sakazume T, Wilding P: Microchip module for blood sample preparation and nucleic acid amplification reactions. Genome Res 2001, 11:405-412.
16. Umek RM, Lin SW, Vielmetter J, Terbrueggen RH, Irvine B, Yu CJ, Kayyem JF, Yowanto H, Blackburn GF, Farkas DH et al: Electronic detection of nucleic acids: a versatile platform for molecular diagnostics. J Mol Diagn 2001, 3:74-84.
17. Lagally ET, Medintz I, Mathies RA: Single-molecule DNA amplification and analysis in an integrated microfluidic device- Anal Chem 2001, 73:565-570.
18. Belgrader P, Hansford D, Kovacs GT, Venkateswaran K, Mariella R Jr, Milanovich F, Nasarabadi S, Okuzumi M, Pourahmadi F, Northrup MA: A minisonicator to rapidly disrupt bacterial spores for DNA analysis. Anal Chem 1999, 71:4232-4236.
19. Taylor MT, Belgrader P, Furman BJ, Pourahmadi F, Kovacs GT, Northrup MA: Lysing bacterial spores by sonication through a flexible interface in a microfluidic system. Anal Chem 2001, 73:492-496.
20. Jones M, Alland D, Marras SA, El-Hajj HH, Taylor MT, McMillan B: Rapid and sensitive detection of Mycobacterium DNA using Cepheid SmartCycler and tube lysis system. Clin Chem 2001, 47:1917-1918.
21. Wolk DM, Persing DH: Clinical microbiology: looking ahead. In Manual of Commercial Methods in Clinical Microbiology. Edited by Truant AL. ASM Press; 2002:429-450.
22. Cockerill FR, Smith TF: Rapid-cycle real-time PCR: a revolution for clinical microbiology. ASM News 2002, 68:77-83. This is an excellent minireview on real-time PCR technologies.
23. Bergeron MG, Ke D, Ménard C, Picard FJ, Gagnon M, Bernier M, Ouellette M, Roy PH, Marcoux S, Fraser WD: Rapid detection of group B streptococci in pregnant women at delivery. N Engl J Med 2000, 343:175-179.
24. Fluit AC, Visser MR, Schmitz FJ: Molecular detection of antimicrobial resistance. Clin Microbiol Rev 2001, 14:836-871.
25. El-Hajj HH, Marras SA, Tyagi S, Kramer FR, Alland D: Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J Clin Microbiol 2001, 39:4131-4137.
26. Mikhailovich V, Lapa S, Gryadunov D, Sobolev A, Strizhkov B, Chernyh N, Skotnikova O, Irtuganova O, Moroz A, Litvinov V et al.: Identification of rifampin-resistant Mycobacterium tuberculosis strains by hybridization, PCR, and ligase detection reaction on oligonucleotide microchips. J Clin Microbiol 2001, 39:2531-2540.
27. Westin L, Miller C, Vollmer D, Canter D, Radtkey R, Nerenberg M, O'Connell JP: Antimicrobial resistance and bacterial identification utilizing a microelectronic chip array. J Clin Microbiol 2001, 39:1097-1104.
28. Sokurenko EV, Tchesnokova V, Yeung AT, Oleykowski CA, Trintchina E, Hughes KT, Rashid RA, Brint JM, Moseley SL, Lory S: Detection of simple mutations and polymorphisms in large genomic regions. Nucleic Acids Res 2001, 29:E111.
29. Howorka S, Cheley S, Bayley H: Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol 2001, 19:636-639.
30. Jonasson J, Olofsson M, Monstein HJ: Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 2002, 110:263-272.
31. Hawkins TL, Detter JC, Richardson PM: Whole genome amplification - applications and advances. Curr Opin Biotechnol 2002, 13:65-67.
32. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Kaczmarski EB, Fox AJ: Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 2000, 38:1747-1752.
33. Nadkarni MA, Martin FE, Jacques NA, Hunter N: Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 2002, 148:257-266.
34. van der Zee A, Peeters M, de Jong C, Verbakel H, Crielaard JW, Claas EC, Templeton KE: Qiagen DNA extraction kits for sample preparation for Legionella PCR are not suitable for diagnostic purposes. J Clin Microbiol 2002, 40:1126.
35. Millar BC, Xu J, Moore JE: 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.
36. Nikkari S, McLaughlin IJ, Bi W, Dodge DE, Relman DA: Does blood of healthy subjects contain bacterial ribosomal DNA? J Clin Microbiol 2001, 39:1956-1959.
37. Ludwig W, Schleifer KH: How quantitative is quantitative PCR with respect to cell counts? Syst Appl Microbiol 2000, 23:556-562.
38. Turenne CY, Tschetter L, Wolfe J, Kabani A: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J Clin Microbiol 2001, 39:3637-3648.
39. Garrett PE: Quality control for nucleic acid tests: common ground and special issues. J Clin Virol 2001, 20:15-21.
40. Niesters HG: Standardization and quality control in molecular diagnostics. Expert Rev Mol Diagn 2001, 1:129-131.
41. 2 gas thermocycler. Genet Eng News 2002, 22:42-43.
42. Giordano BC, Ferrance J, Swedberg S, Huhmer AF, Landers JP: Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds. Anal Biochem 2001, 291:124-132.
43. Ghadessy FJ, Ong JL, Holliger P: Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 2001, 98:4552-4557.
44. Doern GV, Vautour R, Gaudet M, Levy B: Clinical impact of rapid in vitro susceptibility testing and bacterial identification. J Clin Microbiol 1994, 32:1757-1762.
45. Barenfanger J: Significantly reduced variable costs, mortality, and length of stay with timely microbiologic procedures. Am Clin Lab 2001, 20:26-31.
46. Barenfanger J, Drake C, Kacich G: Clinical and financial benefits of rapid bacterial identification and antimicrobial susceptibility testing. J Clin Microbiol 1999, 37:1415-1418.
47. Barenfanger J, Short MA, Groesch AA: Improved antimicrobial interventions have benefits. J Clin Microbiol 2001, 39:2823-2828.
48. Page B, Petrich A, Stevens D, Luinstra K, Callery S, Gafni A, Mahony J, Chernesky M, Groves D: Training costs and investment payback of implementing molecular diagnostics for identification of vancomycin-resistant enterococci in a clinical microbiology laboratory. Diagn Microbiol Infect Dis 2002, 42:91-97.