Hostname: page-component-745bb68f8f-cphqk Total loading time: 0 Render date: 2025-01-11T02:01:21.623Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular Epidemiology of Nosocomial Infection: Analysis of Chromosomal Restriction Fragment Patterns by Pulsed-Field Gel Electrophoresis

Published online by Cambridge University Press:  21 June 2016

Neil L. Barg  and
Richard V. Goering
Neil L. Barg
Affiliation:
Creighton University School of Medicine, Omaha, Nebraska
Richard V. Goering*
Affiliation:
Creighton University School of Medicine, Omaha, Nebraska
*
Department of Medical Microbiology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178
Get access Rights & Permissions [Opens in a new window]

Extract

The epidemiological analysis of nosocomial pathogens is a subject of long-standing clinical interest. In recent years, molecular techniques have received increasing attention as a means of analyzing epidemiological interrelationships, thus leading to use of the term molecular epidemiology. Since chromosomal DNA represents a fundamental molecule of cellular identity, there has been particular interest in assessing chromosomal similarity as a measure of epidemiological relatedness.

One attractive approach has been to digest chromosomal DNA with restriction enzymes, resulting in a series of different sized fragments that form patterns when comparatively analyzed by agarose gel electrophoresis. In this context, differences in fragment patterns commonly are referred to as restriction-fragment length polymorphisms (RFLPs). Enzymes commonly used to cleave DNA typically recognize numerous sites within the bacterial chromosome. With such enzymes, restriction digestion of DNA from different bacterial isolates results in fragments that are too numerous to compare accurately after conventional agarose gel electrophoresis.

Type
Molecular Hospital Epidemiology
Information
Infection Control & Hospital Epidemiology , Volume 14 , Issue 10 , October 1993 , pp. 595 - 600
Copyright
Copyright © The Society for Healthcare Epidemiology of America 1993 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

1. Chu, G, Vollrath, D, Davis, RW. Separation of large DNA molecules by contourclamped homogeneous electric fields. Science 1986;234:1582–1585.CrossRefGoogle ScholarPubMed
2. Carle, GE Frank, M, Olson, MV. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science 1986;232:65–68.Google Scholar
3. Birren, B, Iai, E. Puhed-field Gel Electropohoresis: a Practical Guide. San Diego, CA: Academic Press Inc.; 1993.Google Scholar
4. Gouby, A, Carles-Nurit, M-J, Bouziges, N, et al. Use of pulsed-field gel electrophoresis for investigation of hospital outbreaks of Acinetobacter baumarmii . J Clin Microbiol 1992;30:1588–1591.CrossRefGoogle Scholar
5. 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;27:2057–2061.10.1128/jcm.27.9.2057-2061.1989CrossRefGoogle ScholarPubMed
6. Yan, W, Taylor, DE. Sizing and mapping of the genome of Campylobacter coli strain UA417R using pulsed-field gel electrophoresis. Gene 1991;101:117–120.10.1016/0378-1119(91)90232-ZCrossRefGoogle ScholarPubMed
7. Taylor, DE, Eaton, M, Yan, W, Chang, N. Genome maps of Campylobacter jejuni and Campylobacter coli . J Bacteriol 1992;174:2332–2337.10.1128/jb.174.7.2332-2337.1992CrossRefGoogle ScholarPubMed
8. Kim, NW, Bingham, H, Khawaja, R, et al. Physical map of Campylobacter jejuni TGH9011 and localization of 10 genetic markers by use of pulsed-field gel electrophoresis. J Bacteriol 1992;174:3494–3498.10.1128/jb.174.11.3494-3498.1992CrossRefGoogle ScholarPubMed
9. Suzuki, Y, Ishihara, M, Funabashi, M, et al. Pulsed-field gel electrophoretic analysis of Campylobacter jejuni DNA for use in euidemiological studies. J Infect 1993:27:39–42.CrossRefGoogle ScholarPubMed
10. Magee, PT, Bowdin, L, Staudinger, J. Comparison of molecular typing methods for Candida albicans . J Clin Microbiol 1992;30:2674–2679.10.1128/jcm.30.10.2674-2679.1992CrossRefGoogle ScholarPubMed
11. Doebbeling, BN, Lehmann, PF, Hollis, RJ, et al. Comparison of pulsed-field gel electrophoresis with isoenzyme profiles as a typing system for Candida tropicalis . Clin Infect Dis 1993;16:377–383.10.1093/clind/16.3.377CrossRefGoogle ScholarPubMed
12. Doi, M, Homma, M, Chindampom, A, Tanaka, K. Estimation of chromosome number and size by pulsed-field gel electrophoresis (PFGE) in medically important Candida species. J Gen Microbiol 1992;138:2243–2251.CrossRefGoogle ScholarPubMed
13. Vazquez, JA, Beckley, A, Donabedian, S, Sobel, JD, Zervos, MJ. Comparison of restriction enzyme analysis versus pulsed- field gradient gel electrophoresis as a typing system for Torulopsis glabrata and Candida species other than C albicans . J Clin Microbiol 1993;31:2021–2030.CrossRefGoogle ScholarPubMed
14. Birkelund, S, Stephens, RS. Construction of physical and genetic maps of Chlamydia trachomatis serovar L2 by pulsed-field gel electrophoresis. J Bacteriol 1992;174:2742–2747.CrossRefGoogle ScholarPubMed
15. Canard, B, Cole, ST Genome organization of the anaerobic pathogen Clostridium perfringens . Proc Natl Acad Sci USA 1989;86:6676–6680.CrossRefGoogle ScholarPubMed
16. Heinzen, R, Stiegler, GL, Whiting, LL, et al. Use of pulsed field gel electrophoresis to differentiate Coxiella burnetii strains. Ann NY Acad Sci 1990;590:504–513.10.1111/j.1749-6632.1990.tb42260.xCrossRefGoogle ScholarPubMed
17. Petter, R, Rozenblatt, S, Schechtman, D, Wellems, TE, Mirelman, D. Electrophoretic karyotype and chromosome assignments for a pathogenic and a nonpathogenic strain of Entamoeba histolytica . Infect Immun 1993;61:3574–3577.CrossRefGoogle Scholar
18. Haertl, R, Bandlow, G. Epidemiological fingerprinting of Enterobacter cloacae by small-fragment restriction endonuclease analysis and pulsed-field gel electrophoresis of genomic restriction fragments. J Clin Microbiol 1993;31:128–133.CrossRefGoogle ScholarPubMed
19. Goering, RV, Winters, MA. Rapid method for epidemiological evaluation of gram-positive cocci by field inversion gel electrophoresis. J Clin Microbiol 1992;30:577–580.10.1128/jcm.30.3.577-580.1992CrossRefGoogle ScholarPubMed
20. Chow, JW, Kuritza, A, Shlaes, DM, et al. Clonal spread of vancomycin-resistant Enterococcus faecium between patients in three hospitals in two states. J Clin Microbiol 1993;31:1609–1611.CrossRefGoogle ScholarPubMed
21. Boyle, JF, Soumakis, SA, Rendo, A, et al. Epidemiologic analysis and genotypic characterization of a nosocomial outbreak of vancomycin-resistant enterococci. J Clin Microbiol 1993;31:1280–1285.10.1128/jcm.31.5.1280-1285.1993CrossRefGoogle ScholarPubMed
22. Gordillo, ME, Singh, KV, Murray, BE. Comparison of ribotyping and pulsed-field gel electrophoresis for subspecies differentiation of strains of Enterococcus faecalis . I Clin Microbiol 1993;31:1570–1574.10.1128/jcm.31.6.1570-1574.1993CrossRefGoogle ScholarPubMed
23. Miranda, AG, Singh, KV, Murray, BE. DNA fingerprinting of Enterococcus faecium by pulsed-field gel electrophoresis may be a useful epidemiologic tool. J Clin Microbiol 1991;29:2752–2757.CrossRefGoogle ScholarPubMed
24. Böhm, H, Karch, H. DNA fingerprinting of Escherichia coli 0157:H7 strains by pulsed-field gel electrophoresis. J Clin Microbiol 1992;30:2169–2172.CrossRefGoogle Scholar
25. Arbeit, RD, Arthur, M, Dunn, R, et al. Resolution of recent evolutionary divergence among Escherichia coli from related lineages: the application of pulsed-field electrophoresis to molecular epidemiology. J Infect Dis 1990;161:230–235.CrossRefGoogle ScholarPubMed
26. Sarafis, K, Isaac-Renton, J. Pulsed-field gel electrophoresis as a method of biotyping of Giardia duodenalis . Am J Trop Med Hyg 1993;48:134–144.CrossRefGoogle ScholarPubMed
27. Kauc, L, Mitchell, M, Goodgal, SH. Size and physical map of the chromosome of Haemophilus influenzae . J Bacteriol 1989;171:2474–2479.10.1128/jb.171.5.2474-2479.1989CrossRefGoogle ScholarPubMed
28. Kauc, L, Goodgal, SH. The size and a physical map of the chromosome of Haemophilus parainfluenzae . Gene 1989;83:377–380.CrossRefGoogle Scholar
29. Schoonmaker, D, Heimberger, T, Birkhead, G. Comparison of ribotyping and restriction enzyme analysis using pulsed-field gel electrophoresis for distinguishing Legionella pneumophila isolates obtained during a nosocomial outbreak. J Clin Microbiol 1992;30:1491–1498.10.1128/jcm.30.6.1491-1498.1992CrossRefGoogle ScholarPubMed
30. Baril, C, Saint Girons, I. Sizing of the Leptospira genome by pulsed-field agarose gel electrophoresis. FEMS Microbiol Lett 1990;71:95–100.CrossRefGoogle Scholar
31. Herrmann, JL, Bellenger, E, Perolat, P, Baranton, G, Girons, IS. Pulsed-field gel electroohoresis of Not I digests of lentospiral DNA A new rapid method of serovar identification. J Clin Microbiol 1992;30:1696–1702.CrossRefGoogle Scholar
32. Zuemer, RL, Ellis, WA, Bolin, CA, Montgomery, JM. Restriction fragment length polymorphisms distinguish Leptospira borgpe-tersenii serovar hardjo type hardjo-bovis isolates from different geographical locations. J Clin Microbiol 1993;31:578–583.Google Scholar
33. Buchrieser, C, Brosch, R, Catimel, B, Rocourt, J. Pulsed-field gel electtophoresis applied for comparing Listeria monocytogenes strains involved in outbreaks. Can J Microbiol 1993;39:395–401.10.1139/m93-058CrossRefGoogle ScholarPubMed
34. Lévy-Frébault, W, Thorel, M-E Varnerot, A, Gicquel, B. DNA polymorphism in Mycobacterium paratuberculosis, “wood pigeon mycobacteria,” and related mycobacteria analyzed by field inversion gel electrophoresis. J Clin Microbiol 1989;27:2823–2826.CrossRefGoogle ScholarPubMed
35. 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;167:1384–1390.10.1093/infdis/167.6.1384CrossRefGoogle ScholarPubMed
36. Coffm, JW, Condon, C, Compston, CA, et al. Use of restriction fragment length polymorphisms resolved by pulsed-field gel electrophoresis for subspecies identification of mycobacteria in the Mycobacterium avium complex and for isolation of DNA probes. J Clin Microbiol 1992;30:1829–1836.CrossRefGoogle Scholar
37. Vamerot, A, Clement, F, Gheorghiu, M, Vincent-Lévy-Frébault, V. Pulsed field gel electrophoresis of representatives of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains. FEMS Microbiol Lett 1992;98:155–160.Google Scholar
38. Ladefoged, SA, Christiansen, G. Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis. J Bacteriol 1992;174:2199–2207.10.1128/jb.174.7.2199-2207.1992CrossRefGoogle ScholarPubMed
39. Wenzel, R, Herrmann, R Phycisal mapping of the Mycoplasma pneumoniae nenome. Nucleic Acids Res 1988;16:8323–8336.10.1093/nar/16.17.8323CrossRefGoogle Scholar
40. Miyata, M, Wang, L, Fukumura, T. Physical mapping of the Mycoplasma capricolum genome. FEMS Microbiol Lett 1991;79:329–334.CrossRefGoogle Scholar
41. Poh, CL, Lau, QC. Subtyping of Neisseria gonorrhoeae auxotype-serovar groups by pulsed-field gel electrophoresis. J Med Microbiol 1993;38:366–370.CrossRefGoogle ScholarPubMed
42. Strathdee, CA, Tyler, SD, Ryan, JA, Johnson, WM, Ashton, FE. Genomic Fingerprinting of Neisseria meningitidis associated with group C meningococcal disease in Canada. J Clin Microbiol 1993;31:2506–2508.CrossRefGoogle Scholar
43. Römling, U, Grothues, D, Koopmann, U, Jahnke, B, Greipel, J, Tümmler, B. Pulsed-field gel electrophoresis analysis of a Pseudomoms aeruginosa pathovar. Electrophoresis 1992;13:646–648.CrossRefGoogle ScholarPubMed
44. Straelens, MJ, Schwam, V, Deplano, A, Baran, D. Genome mactorestriction analysis of diversity and variability of Pseudomonas aeruginosa strains infecting cystic fibrosis patients. J Clin Microbiol 1993;31:2320–2326.CrossRefGoogle Scholar
45. Poh, CL, Yeo, CC, Tay, L. Genome fingerprinting by pulsed-field gel electrophoresis and ribotyping to differentiate Pseudomonas aeruginosa serotype 011 strains, Eur J Clin Microbiol Infect Dis 1992;11:817–822.CrossRefGoogle Scholar
46. Sader, HS, Pignatari, AC, Leme, IL, et al. Epidemiologie typing of multiply drug-resistant Pseudomonas aeruginosa isolated from an outbreak in an intensive care unit. Diagn Microbiol Infect Dis 1993;17:13–18.10.1016/0732-8893(93)90063-DCrossRefGoogle Scholar
47. Anderson, DJ, Kuhns, JS, Vasil, ML, Gerding, DN, Janoff, EN. DNA fingerprinting by pulsed field gel electrophoresis and ribotyping to distinguish Pseudomonas cepacia isolates from a nosocomial outbreak. J Clin Microbiol 1991;29:648–649.CrossRefGoogle ScholarPubMed
48. Roux, V, Drancourt, M, Raoult, D. Determination of genome sizes of Rickettsia spp. within the spotted fever group, using pulsed-field gel electrophoresis. J Bacteriol 1992;174:7455–7457.CrossRefGoogle ScholarPubMed
49. Roux, V, Raoult, D. Genotypic identification and phylogenetic analysis of the spotted fever group rickettsiae by pulsed-field gel electrophoresis. J Bacteriol 1993:175:4895–4904.CrossRefGoogle ScholarPubMed
50. Liu, S-L, Hessel, A, Sanderson, KE. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella typhimurium LT2 determined by double digestion, end labelling, and pulsed-field gel electrophoresis. J Bacteriol 1993;175:4104–4120.CrossRefGoogle ScholarPubMed
51. Soldati, L, Piffaretti, JC. Molecular typing of Shigella strains using pulsed field gel electrophoresis and genome hybridization with insertion sequences. Res Microbiol 1991;142:489–498.CrossRefGoogle ScholarPubMed
52. Brian, MJ, Van, R, Townsend, I, et al. Evaluation of the molecular epidemiology of an outbreak of multiply resistant Shigella sonnei in a day-care center by using pulsed-field gel electrophoresis and Plasmid DNA analysis. J Clin Microbiol 1993;31:2152–2156.CrossRefGoogle Scholar
53. Goering, RV, Bauernfeind, A, Lenz, W, Przyklenk, B. Staphylococcus aureus in patients with cystic fibrosis: An epidemiological analysis using a combination of traditional and molecular methods. Infection 1990;18:57–60.10.1007/BF01644187CrossRefGoogle ScholarPubMed
54. Goering, RV, Duensing, TD. Rapid field inversion gel electrophoresis in combination with an rRNA gene probe in the epidemiological evaluation of staphylococci. J Clin Microbiol 1990;28:426–429.10.1128/jcm.28.3.426-429.1990CrossRefGoogle ScholarPubMed
55. Ichiyama, S, Olita, M, Shimokata, K, Kato, N, Takeuchi, J. Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus . J Clin Microbial 1991;29:2690–2695.CrossRefGoogle ScholarPubMed
56. Inglis, B, El-Adhami, W, Stewart, PR. Methicillin-sensitive and -resistant homologues of Staphylococcus aureus occur together among clinical isolates. J Infect Dis 1993;167:323–328.10.1093/infdis/167.2.323CrossRefGoogle ScholarPubMed
57. Prevost, G, Jaulhac, B, Piemont, Y. DNA fingerprinting by pulsed-field gel electrophoresis is more effective than ribotyping in distinguishing among methicillin-resistant Staphylococcus aureus isolates. J Clin Microbiol 1992;30:967–973.CrossRefGoogle ScholarPubMed
58. Saulnier, P, Bourneix, C, Prevost, G, Andremont, A. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus . J Clin Microbiol 1993;31:982–985.CrossRefGoogle ScholarPubMed
59. Schlichting, C, Branger, C, Fournier, J-M, et al. Typing of Stuphylococcusaureus by pulsed-field gel electrophoresis, zymotyping, capsular typing, and phage typing: resolution of clonal relationships. J Clin Microbiol 1993;31:227–232.CrossRefGoogle ScholarPubMed
60. Shayegani, M, Parsons, LM, Waring, AL, et al. Molecular related-ness of Staphylococcus epidermidis isolates obtained during a platelet transfusion-associated episode of sepsis. J Clin Microbiol 1991;29:2768–2773.10.1128/jcm.29.12.2768-2773.1991CrossRefGoogle Scholar
61. Struelens, MJ, Deplano, A, Godard, C, Maes, N, Serruys, E. Epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus by macrorestriction analysis of genomic DNA by using pulsed-field gel electrophoresis. J Clin Microbiol 1992;30:2599–2605.CrossRefGoogle ScholarPubMed
62. Udo, EE, Grubb, WB. Genetic analysis of methicillin-resistant Staphylococcus aureus from a Nigerian hospital. J Med Microbiol 1993;38:203–208.CrossRefGoogle ScholarPubMed
63. Wanger, AR, Morris, SL, Ericsson, C, Singh, KV, LaRocco, MT Latex agglutination-negative methicillin-resistant Staphylococcus aureus recovered from neonates: epidemiologic features and comparison of typing methods. J Clin Microbiol 1992;30:2583–2588.10.1128/jcm.30.10.2583-2588.1992CrossRefGoogle ScholarPubMed
64. 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. Med Microbiol Lett 1993;2:33–41.Google Scholar
65. Witte, W, Cuny, CH, Claus, H. Clonal relatedness of Staphylococcus aureus strains from infections in humans as deduced from genomic DNA fragment patterns. Med Microbiol Lett 1993;2:72–79.Google Scholar
66. Martin, DR, Single, LA. Molecular epidemiology of group A streptococcus M type 1 infections. J Infect Dis 1993;167:1112–1117.10.1093/infdis/167.5.1112CrossRefGoogle ScholarPubMed
67. Gordillo, ME, Singh, KV, Baker, CJ, Murray, BE. Typing of group B streptococci: comparison of pulsed-field gel electrophoresis and conventional electrophoresis. J Clin Microbiol 1993;31:1430–1434.10.1128/jcm.31.6.1430-1434.1993CrossRefGoogle Scholar
68. Khattak, MN, Burnie, JP, Matthews, RC, Oppenheim, BA. Clamped homogeneous electric field gel electrophoresis typing of Torulopsis glabrata isolates causing nosocomial infections, J Clin Microbiol 1992;30:2211–2215.CrossRefGoogle ScholarPubMed
69. Lucier, TS, Brubaker, RR. Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in Yersinia pestis by pulsed-field gel electrophoresis. J Bacteriol 1992;174:2078–2086.10.1128/jb.174.7.2078-2086.1992CrossRefGoogle ScholarPubMed
70. Patel, AH, Foster, TJ, Pattee, PA. Physical and genetic mapping of the protein A gene in the chromosome of Staphylococcus aureus 8325-4 . J Gen Microbiol 1989;135:1799–1807.Google ScholarPubMed
71. Lina, B, Bes, M, Vandenesch, F et al. Role of bacteriophages in genomic variability of related coagulasenegative staphylococci. FEMS Microbiol Lett 1993;109:273–278.CrossRefGoogle ScholarPubMed
72. Dice, LR. Measures of the amount of ecologie association between species. Ecology 1945;26:297–302.10.2307/1932409CrossRefGoogle Scholar
73. Peterson, LR, Petzel, RA, Clabots, CR, Fasching, CE, Gerding, DN. Medical technologists using molecular epidemiology as part of the infection control team. Diagn Microbiol Infect Dis 1993;16:303–311.10.1016/0732-8893(93)90080-QCrossRefGoogle ScholarPubMed