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How to Select and Interpret Molecular Strain Typing Methods for Epidemiological Studies of Bacterial Infections A Review for Healthcare Epidemiologists

Published online by Cambridge University Press:  02 January 2015

Fred C. Tenover ,
Robert D. Arbeit ,
Richard V. Goering  and
Molecular Typing Working Group of the Society for Healthcare Epidemiology of America
Fred C. Tenover*
Affiliation:
Hospital Infections Program, Centers for Disease Control and Prevention, Atlanta, Georgia
Robert D. Arbeit
Affiliation:
The Boston Veterans' Affairs Medical Center, Boston, Massachusetts
Richard V. Goering
Affiliation:
The Department of Medical Microbiology, Creighton University, Creighton, Nebraska
*
Nosocomial Pathogens Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333
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Abstract

Strain typing is an integral part of epidemiological investigations of nosocomial infections. Methods for distinguishing among bacterial strains have improved dramatically over the last 5 years, due mainly to the introduction of molecular technology. Although not all molecular techniques are equally effective for typing all organisms, pulsed-field gel electrophoresis is the technique currently favored for most nosocomial pathogens. Criteria to aid epidemiologists in interpreting results have been published. Nucleic acid amplification-based typing methods also are applicable to many organisms and can be completed within a single day, but interpretive criteria still are under debate. Strain typing cannot be used to replace a sound epidemiological investigation, but serves as a useful adjunct to such investigations.

Type
SHEA Position Paper
Information
Infection Control & Hospital Epidemiology , Volume 18 , Issue 6 , June 1997 , pp. 426 - 439
Copyright
Copyright © The Society for Healthcare Epidemiology of America 1997

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References

1. Emori, TG, Gaynes, RP. An overview of nosocomial infections, including the role of the microbiology laboratory. Clin Microbiol Rev 1993;6:428–442.CrossRefGoogle ScholarPubMed
2. Olive, KE, Berk, SL. Infections in the nursing home. Clin Geriatr Med 1992;8:821–834.CrossRefGoogle ScholarPubMed
3. Maki, DG, Rhame, FS, Mackel, DC, Bennett, JV. Nationwide epidemic of septicemia caused by contaminated intravenous products, I: epidemiologic and clinical features. Am J Med 1976;60:471–485.CrossRefGoogle ScholarPubMed
4. Tenover, FC, Hughes, JM. The challenges of emerging infectious diseases: development and spread of multiply resistant bacterial pathogens. JAMA 1996;275:300–304.Google Scholar
5. Hospital Infection Control Practices Advisory Committee, Centers for Disease Control and Prevention. Recommendations for preventing the spread of vancomycin resistance. Infect Control Hosp Epidemiol 1995;16:105–113.CrossRefGoogle Scholar
6. Arbeit, RD. Laboratory procedures for the epidemiologic analysis of microorganisms. In: Murray, PR, Baron, EJ, Pfaller, MA, Tenover, FC, Yolken, RH, eds. Manual of Clinical Microbiology. 6th ed. Washington, DC: American Society for Microbiology; 1995:190–208.Google Scholar
7. El-Ahami, W, Roberts, L, Vickery, A, et al. Epidemiological analysis of a methicillin-resistant Staphylococcus aureus outbreak using restriction fragment length polymorphisms of genomic DNA. J Gen Microbiol 1991;137:2713–2720.Google Scholar
8. Montecalvo, MA, Horowitz, H, Gedris, C, et al. Outbreak of vancomycin-, ampicillin-, and aminoglycoside-resistant Enterococcus faecium bacteremia in an adult oncology unit. Antimicrob Agents Chemother 1994;38:1363–1367.CrossRefGoogle Scholar
9. Sader, HS, Pignatari, AC, Leme, IL, et al. Epidemiologic typing of multiply drug-resistant Pseudomonas aeruginosa isolated from an outbreak in an intensive care unit. Diagn Microbiol Infect Dis 1993;17:13–18.CrossRefGoogle Scholar
10. Gouby, A, Neuwirth, C, Bourg, G, et al. Epidemiological study by pulsed-field gel electrophoresis of an outbreak of extended-spectrum β-lactamase-producing Klebsiella pneumoniae in a geriatric hospital. J Clin Microbiol 1994;32:301–305.CrossRefGoogle Scholar
11. Tenover, FC, Arbeit, RD, Goering, RV, et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995;33:2233–2239.Google Scholar
12. Aber, RC, Macke, DC. Epidemiologic typing of nosocomial microorganisms. Am J Med 1981;70:899–905.CrossRefGoogle ScholarPubMed
13. Swaminathan, B, Matar, GM. Molecular typing methods: definition, applications, and advantages. In: Persing, DH, Smith, TF, Tenover, FC, White, TJ, eds. Diagnostic Molecular Microbiology: Principles and Applications. Washington, DC: American Society for Microbiology; 1993:26–50.Google Scholar
14. Goering, RV. Molecular epidemiology of nosocomial infection: analysis of chromosomal restriction fragment patterns by pulsed-field gel electrophoresis. Infect Control Hosp Epidemiol 1993;14:595–600.Google Scholar
15. Musser, JM. Molecular population genetic analysis of emerging bacterial pathogens: selected insights. Emerg Infect Dis 1996;2:1–17.CrossRefGoogle ScholarPubMed
16. Kreiswirth, B, Kornblum, J, Arbeit, RD, et al. Evidence for a clonal origin of methicillin resistance in Staphylococcus aureus . Science 1993;259:227–230.CrossRefGoogle ScholarPubMed
17. Tenover, FC, Arbeit, R, Archer, G, et al. Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus . J Clin Microbiol 1994;32:407–415.Google Scholar
18. Kato, H, Kato, N, Watanabe, K, et al. Application of typing by pulsed-field gel electrophoresis to the study of Clostridium difficile in a neonatal intensive care unit. J Clin Microbiol 1994;32:2067–2070.CrossRefGoogle Scholar
19. Maslow, JN, Slutsky, AM, Arbeit, RD. The application of pulsed- field gel electrophoresis to molecular epidemiology. In: Persing, DH, Smith, TF, Tenover, FC, White, TJ, eds. Diagnostic Molecular Microbiology: Principles and Applications. Washington, DC: American Society of Microbiology; 1993:563–572.Google Scholar
20. van Belkum, A, Meis, J. Polymerase chain reaction-mediated genotyping in microbial epidemiology. Clin Infect Dis 1994;18:1018–1019.Google Scholar
21. Schwartz, DN, Schable, B, Tenover, FC, et al. Leptotrichia buccalis bacteremia in patients treated in a single bone marrow transplant unit. Clin Infect Dis 1995;20:762–767.CrossRefGoogle Scholar
22. Tenover, FC, McGowan, JE Jr. Reasons for the emergence of antibiotic resistance. Am J Med Sci 1996;311:9–16.Google Scholar
23. Davies, J. Inactivation of antibiotics and the dissemination of resistance genes. Science 1994;264:375–382.CrossRefGoogle ScholarPubMed
24. Nakamura, S, Nakamura, M, Kojima, T, et al. gyrA and gyrB mutations in quinolone resistant strains of Escherichia coli . Antimicrob Agents Chemother 1989;33:254–255.Google Scholar
25. Locksley, RM, Cohen, ML, Quinn, TC, et al. Multiply antibiotic-resistant Staphylococcus aureus: introduction, transmission, and evolution of nosocomial infection. Ann Intern Med 1982;97:317–324.CrossRefGoogle ScholarPubMed
26. Mickelsen, PA, Plorde, JJ, Gordon, KP, et al. Instability of antibiotic resistance in a strain of Staphylococcus epidermidis isolated from an outbreak of prosthetic valve endocarditis. J Infect Dis 1985;152:50–58.CrossRefGoogle Scholar
27. Olsen, JE, Skov, MN, Threlfall, EJ, et al. Clonal lines of Salmonella enterica serotype enteritidis documented by IS200-, ribo-, pulsed-field gel electrophoresis and RFLP typing. J Med Microbiol 1994;40:15–22.Google Scholar
28. McDougal, LK, Rasheed, JK, Biddle, JW, Tenover, FC. Identification of multiple clones of extended-spectrum cephalosporin-resistant Streptococcus pneumoniae in the United States. Antimicrob Agents Chemother 1996;39:2282–2288.Google Scholar
29. Schaberg, DR, Tompkins, LS, Falkow, S. Use of agarose gel electrophoresis of plasmid deoxyribonucleic acid to fingerprint gram-negative bacilli. J Clin Microbiol 1981;13:1105–1110.Google Scholar
30. Taylor, DN, Wachsmuth, IK, Shangkuan, Y, et al. Salmonellosis associated with marijuana—a multistate outbreak traced by plasmid fingerprinting. N Engl J Med 1982;306:1249–1253.Google Scholar
31. Tenover, FC. Plasmid fingerprinting: a tool for bacterial strain identification and surveillance of nosocomial and community-acquired infections. Clin Lab Med 1985;5:413–436.CrossRefGoogle ScholarPubMed
32. Fornasini, M, Reeves, RR, Murray, BE, et al. Trimethoprim-resistant Escherichia coli in households of children attending day care centers. J Infect Dis 1992;166:326–330.CrossRefGoogle ScholarPubMed
33. Pfaller, MA, Wakefield, DS, Hollis, R, et al. The clinical microbiology laboratory as an aid in infection control. The application of molecular techniques in epidemiologic studies of methicillin-resistant Staphylococcus aureus . Diagn Microbiol Infect Dis 1991;14:209–214.CrossRefGoogle ScholarPubMed
34. Tompkins, LS, Plorde, JJ, Falkow, S. Molecular analysis of R-factors from multiresistant nosocomial isolates. J Infect Dis 1980;141:625–636.CrossRefGoogle ScholarPubMed
35. Carles-Nuit, MJ, Christophile, B, Broche, S, et al. DNA polymorphisms in methicillin-susceptible and methicillin-resistant strains of Staphylococcus aureus . J Clin Microbiol 1992;30:2092–2096.Google Scholar
36. Schwartz, DC, Cantor, CR. Separation of yeast chromosome-sized DNAs by pulsed-field gel electrophoresis. Cell 1984;37:67–75.CrossRefGoogle Scholar
37. Clabots, CR, Johnson, S, Olson, MM, et al. Acquisition of Clostridium difficile by hospitalized patients: evidence for colonized new admissions as a source of infection. J Infect Dis 1992;166:561–567.Google Scholar
38. Sambrook, J, Fritsch, EF, Maniatis, T. Molecular Cloning—A Laboratory Manual. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Press; 1989.Google Scholar
39. Stull, TL, LiPuma, JJ, Edlind, TD. A broad-spectrum probe for molecular epidemiology of bacteria: ribosomal RNA. J Infect Dis 1988;157:280–286.CrossRefGoogle ScholarPubMed
40. Arthur, M, Arbeit, RD, Kim, C, et al. Restriction fragment length polymorphisms among uropathogenic Escherichia coli isolates: pap-related sequences compared with rrn operons. Infect Immun 1990;58:471–479.Google Scholar
41. Kristjansson, M, Samore, MH, Gerding, DN, et al. Comparison of restriction endonuclease analysis, ribotyping, and pulsed-field gel electrophoresis for molecular differentiation of Clostridium difficile strains. J Clin Microbiol 1994;32:1963–1969.Google Scholar
42. Gordillo, ME, Singh, KV, Murray, BE. Comparison of ribotyping and pulsed-field gel electrophoresis for subspecies differentiation of strains of Enterococcus faecalis . J Clin Microbiol 1993;31:1570–1574.Google Scholar
43. van Embden, JDA, Cave, MD, Crawford, JT, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993;31:406–409.Google Scholar
44. Small, PM, Hopewell, PC, Singh, SP, et al. The epidemiology of tuberculosis in San Francisco: a population-based study using conventional and molecular methods. N Engl J Med 1994;330:1703–1709.CrossRefGoogle Scholar
45. Persing, DH. In vitro nucleic acid amplification techniques. In: Persing, DH, Smith, T, Tenover, FC, White, T, eds. Diagnostic Molecular Microbiology: Principles and Applications. Washington, DC: American Society for Microbiology; 1993:51–87.Google Scholar
46. Welsh, J, McClelland, M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 1990;18:7213–7218.Google Scholar
47. Williams, JGK, Kubelik, AR, Livak, KJ, et al. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990;18:6531–6535.CrossRefGoogle ScholarPubMed
48. van Belkum, A. DNA fingerprinting of medically important microorganisms by use of PCR. Clin Microbiol Rev 1994;7:174–184.Google Scholar
49. Killgore, GE, Kato, H. Use of arbitrary primed PCR to type Clostridium difficile and comparison of results with those by immunoblot typing. J Clin Microbiol 1994;32:1591–1593.Google Scholar
50. van Belkum, A, Kluytmans, J, van Leeuwen, W, et al. Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains. J Clin Microbiol 1995;33:1537–1547.Google Scholar
51. Tyler, KD, Wang, G, Tyler, SD, Johnson, WM. Factors affecting reliability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J Clin Microbiol 1997;35:339–346.CrossRefGoogle ScholarPubMed
52. DuBose, RF, Dykhuiszen, DE, Hartl, DL. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli . Proc Natl Acad Sci USA 1988;85:7036–7040.Google Scholar
53. Dean, D, Patton, M, Stephens, RS. Direct sequence evaluation of the major outer membrane protein gene variant regions of Chlamydia trachomatis subtypes D′ I′, and L2′. Infect Immun 1991;59:1579–1582.Google Scholar
54. Winters, MA, Goering, RV, Boon, SE, et al. Epidemiological analysis of methicillin-resistant Staphylococcus aureus comparing plasmid typing with chromosomal analysis by field inversion gel electrophoresis. Medical Microbiology Letters 1993;2:33–41.Google Scholar
55. Goering, RV, Winters, MA. A rapid method for the evaluation of chromosomal DNA from gram-positive cocci by field-inversion gel electrophoresis. J Clin Microbiol 1992;30:577–580.Google Scholar
56. Lefevre, JC, Faucon, G, Sicard, AM, Gasc, AM. DNA fingerprinting of Streptococcus pneumoniae strains by pulsed-field gel electrophoresis. J Clin Microbiol 1993;31:2724–2728.Google Scholar
57. Lund, E, Henrichsen, J. Laboratory diagnosis, serology and epidemiology of Streptococcus pneumoniae . Methods Microbiol 1978;12:241–262.Google Scholar
58. Murray, BE, Singh, KV, Heath, JD, et al. Comparison of genomic DNAs of different enterococcal isolates using restriction endonucleases with infrequent recognition sites. J Clin Microbiol 1990;28:2059–2063.Google Scholar
59. Versalovic, J, Koeuth, T, Lupski, JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991;19:6823–6831.CrossRefGoogle ScholarPubMed
60. Beltran, P, Musser, JM, Helmuth, R, et al. Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S choleraesuis, S derby, S dublin, S enteritidis, S heidelberg, S infantis, S newport, and S typhimurium . Proc Natl Acad Sci 1988;85:7753–7757.Google Scholar
61. Litwin, CM, Storm, AL, Chipowsky, S, Ryan, KJ. Molecular epidemiology of Shigella infections: plasmid profiles, serotype correlation, and restriction endonuclease analysis. J Clin Microbiol 1991;29:104–108.Google Scholar
62. Struelens, MJ, Schwam, V, Deplano, A, Baran, D. Genome macrorestriction analysis of diversity and variability of Pseudomonas aeruginosa strains infecting cystic fibrosis patients. J Clin Microbiol 1993;31:2320–2326.Google Scholar
63. Allardet-Servent, A, Bouziges, N, Carles-Nurit, M-J, et al. Use of low-frequency-cleavage restriction endonucleases for DNA analysis in epidemiological investigations of nosocomial bacterial infections. J Clin Microbiol 1989;27:2057–2061.CrossRefGoogle ScholarPubMed
64. Grundmann, H, Schneider, C, Hartung, D, et al. Discriminatory power of three DNA-based typing techniques for Pseudomonas aeruginosa . J Clin Microbiol 1995;33:528–534.Google Scholar
65. Pradella, S, Pletschette, M, Mantey-Stiers, F, Bautsch, W. Macrorestriction analysis of Pseudomonas aeruginosa in colonized burn patients. Eur J Clin Microbiol Infect Dis 1994;13:122–128.Google Scholar
66. Römling, U, Fiedler, B, Bosshammer, J, et al. Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis. J Infect Dis 1994;170:1616–1621.Google Scholar
67. Gouby, A, Carles-Nurit, M-J, Bouziges, N, et al. Use of pulsed-field gel electrophoresis for investigation of hospital outbreaks of Acinetobacter baumanii . J Clin Microbiol 1992;30:1588–1591.Google Scholar
68. Yuk-Fong Liu, P, Shi, Z, Lau, Y, et al. Comparison of different PCR approaches for characterization of Burkholderia (Pseudomonas) cepacia isolates. J Clin Microbiol 1995;33:3304–3307.Google Scholar
69. Cave, MD, Eisenach, KD, McDermott, PF, et al. IS6110: conservation of sequence in the Mycobacterium tuberculosis complex and its utilization in DNA fingerprinting. Mol Cell Probes 1991;5:73–80.Google Scholar
70. Friedman, CR, Stoeckle, MY, Johnson, WD, Riley, LW. Double-repetitive-element PCR method for subtyping Mycobacterium tuberculosis clinical isolates. J Clin Microbiol 1995;33:1383–1384.Google Scholar
71. Arbeit, RD, Slutsky, A, Barber, TW, et al. Genetic diversity among strains of Mycobacterium avium causing monoclonal and polyclonal bacteremia in patients with AIDS. J Infect Dis 1993;167:1384–1390.Google Scholar
72. Wallace, RJ Jr, Zhang, Y, Brown, BA, et al. DNA large restriction fragment patterns of sporadic and epidemic nosocomial strains of Mycobacterium chelonae and Mycobacterium abscessus . J Clin Microbiol 1993;31:2697–2701.Google Scholar
73. McGowan, JE Jr, Metchock, B. Infection control epidemiology and clinical microbiology. In: Murray, PR, Baron, EJ, Pfaller, MA, Tenover, FC, Yolken, RH, eds. Manual of Clinical Microbiology. 6th ed. Washington, DC: American Society for Microbiology; 1995:182–189.Google Scholar
74. van Belkum, A, Melchers, W, de Pauw, BE, et al. Genotypic characterization of sequential Candida albicans isolates from fluconazole-treated neutropenic patients. J Infect Dis 1994;169:1062–1070.Google Scholar
75. Struelens, MJ, Members of the European Study Group on Epidemiological Markers. Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin Microbiol Infect 1996;2:2–11.CrossRefGoogle ScholarPubMed