Skip to main content
SpringerLink
Log in

Pulsed-Field Gel Electrophoresis

  • Chapter
Advanced Techniques in Diagnostic Microbiology

Abstract

The field of molecular diagnostics has rapidly expanded to include technology for accurate and timely determination of clonal relatedness of microorganisms of epidemiological interest as well as the detection of infectious agents in real-time. The predominant technique used for strain characterization has been pulsed-field gel electrophoresis (PFGE), first developed in the early 1980s, to genotype microorganisms by electrophoretic separation of chromosomal DNA by molecular weight (Van der Ploeg et al., 1984). Over the years, this technology has proved to be a powerful tool used alone or in conjunction with restriction endonuclease digestion of the DNA in order to understand the evolution of antimicrobial resistance generated within a single clone and to determine genetic relatedness among microbial strains in industrial and agricultural settings, as well as health care associated epidemiologic investigations. This chapter will discuss the principle characteristics and the clinical applications of PFGE technology, including examples that illustrate its successful application to epidemiology. The strengths and limitations of PFGE are discussed as well as alternative strain-typing methods.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 189.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aires de Sousa, M., & de Lencastre, H. (2004). Bridges from hospitals to the laboratory: genetic portraits of methicillin-resistant Staphylococcus aureus clones. FEMS Immunol Med Microbiol, 40, 101–111.

    Article  PubMed  CAS  Google Scholar 

  • Arbeit, R.D., Arthur, M., Dunn, R., Kim, C., Selander, R.K., & Goldstein, R. (1990). Resolution of recent evolutionary divergence among Escherichia coli from related lineages: the application of pulsed field electrophoresis to molecular epidemiology. J Infect Dis, 161, 230–235.

    PubMed  CAS  Google Scholar 

  • Baba, T., Takeuchi, F., Kuroda, M., Yuzawa, H., Aoki, K., Oguchi, A., Nagai, Y., Iwama, N., Asano, K., Naimi, T., Kuroda, H., Cui, L., Yamamoto, K., & Hiramatsu, K. (2002). Genome and virulence determinants of high virulence community-acquired MRSA. Lancet, 25, 1819–1827.

    Article  Google Scholar 

  • Bennett, J.E., Izumikawa, K., & Marr, K.A. (2004). Mechanism of increased fluconazole resistance in Candida glabrata during prophylaxis. Antimicrob Agents Chemother, 48, 1773–1777.

    Article  PubMed  CAS  Google Scholar 

  • Blanc, D.S., Francioli, P., & Hauser, P.M. (2002). Poor value of pulsed-field gel electrophoresis to investigate long-term scale epidemiology of methicillin-resistant Staphylococcus aureus. Infect Genet Evolution, 2, 145–148.

    Article  CAS  Google Scholar 

  • Cantor, C.R., Gaal, A., & Smith, C.L. (1988). High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 3. Effect of electrical field shape. Biochemistry, 27, 9216–9221.

    Article  PubMed  CAS  Google Scholar 

  • Carle, G.F., Frank, M., & Olson, M. V. (1986). Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science, 232, 65–68.

    Article  PubMed  CAS  Google Scholar 

  • Carle, G.F., & Olson, M. V. (1984). Separation of chromosomal DNA molecules from yeast by orthogonal-field-alteration gel electrophoresis. Nucleic Acids Res, 12, 5647–5664.

    Article  PubMed  CAS  Google Scholar 

  • Centers for Disease Control and Prevention. (1999). Four pediatric deaths from communityacquired methicillin-resistant Staphylococcus aureus—Minnesota and North Dakota, 1997–1999. Morbid Mortal Weekly Rep, 48, 707–710.

    Google Scholar 

  • Centers for Disease Control and Prevention. (2004). Day care-related outbreaks of rhamnose-negative Shigella sonnei—six states, June 2001-March 2003. Morbid Mortal Weekly Rep, 53, 60–63.

    Google Scholar 

  • Chu, G., Vollrath, D., & Davis, R. W. (1986). Separation of large DNA molecules by contourclamped homogeneous electric fields. Science, 234, 1582–1585.

    Article  PubMed  CAS  Google Scholar 

  • Chung, M., de Lencastre, H., Matthews, P., Tomasz, A., Adamsson, I., Aires de Sousa, M., Camou, T., Cocuzza, C., Corso, A., Couto, I., Dominguez, A., Gniadkowski, M., Goering, R., Gomes, A., Kikuchi, K., Marchese, A., Mato, R., Melter, O., Oliveira, D., Palacio, R., Sa-Leao, R., Santos Sanches, I., Song, J.H., Tassios, P.T., & Villari, P. (2000). Molecular typing of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis: comparison of results obtained in a multi-laboratory effort using identical protocols and MRSA strains. Microbiol Drug Resist, 6, 189–198.

    Article  CAS  Google Scholar 

  • Clark, S.M., Lai, E., Birren, B. W., & Hood, L. (1988). A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields. Science, 241, 1203–1205.

    Article  PubMed  CAS  Google Scholar 

  • Decludt, B., Campese, C., Che, D., Jarraud, S., & Etienne, J. (2004). Clusters of travel associated legionnaires’ disease in France, September 2001–August 2003. Eurosurveillance, 9, 7–8.

    Google Scholar 

  • Duck, W.M., Steward, C.D., Banerjee, S.N., McGowan, J.E. Jr., & Tenover, F.C. (2003). Optimization of computer software settings improves accuracy of pulsed-field gel electrophoresis macrorestriction fragment pattern analysis. J Clin Microbiol, 41, 3035–3042.

    Article  PubMed  CAS  Google Scholar 

  • Durmaz, R., Durmaz, B., Bayraktar, M., Ozerol, I.H., Kalcioglu, M.T., Aktas, E., & Cizmeci, Z. (2003). Prevalence of group A streptococcal carriers in asymptomatic children and clonal relatedness among isolates in Malatya, Turkey. J Clin Microbiol, 41, 5285–5287.

    Article  PubMed  CAS  Google Scholar 

  • el-Mohandes, A.E., Johnson-Robbins, L., Keiser, J.F., Simmens, S.J., & Aure, M. V. (1994). Incidence of Candida parapsilosis colonization in an intensive care nursery population and its association with invasive fungal disease. Pediatr Infect Dis J, 13, 520–524.

    Article  PubMed  CAS  Google Scholar 

  • Espinel-Ingroff, A., Vazquez, J.A., Boikov, D., & Pfaller, M.A. (1999). Evaluation of DNAbased typing procedures for strain categorization of Candida spp. Diagn Microbiol Infect Dis, 33, 231–239.

    Article  PubMed  CAS  Google Scholar 

  • Fiett, J., Kucharczyk, K., & Gniadkowski, M. (2004). A new method of DNA preparation for pulsed-field gel electrophoresis analysis. J Microbiol Methods, 59, 433–436.

    Article  PubMed  CAS  Google Scholar 

  • Gardiner, K., Laas, W., & Patterson, D. (1986). Fractionation of large mammalian DNA restriction fragments using vertical pulsed-field gradient gel electrophoresis. Somatic Cell Mol Genet, 12, 185–195.

    Article  PubMed  CAS  Google Scholar 

  • Gautom, R.K. (1997). Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other gram-negative organisms in 1 day. J Clin Microbiol, 35, 2977–2980.

    PubMed  CAS  Google Scholar 

  • Goering, R. V. (1998). The molecular epidemiology of nosocomial infection. An overview of principles, application and interpretation. In: Specter, S., Bendirelli, M., & Freedman, H., eds. Rapid Detection of Infectious Agents, Plenum Press, New York, pp. 131–157.

    Google Scholar 

  • Goering, R. V. (2000). Molecular strain typing for the clinical laboratory: current application and future direction. Clin Microbiol News, 22, 169–173.

    Article  Google Scholar 

  • Goering, R. V. (2004). Pulsed-field gel electrophoresis. In: Persing, D.H., Tenover, F.C., Versalovic, J. et al. Molecular Microbiology: Diagnostic Principles and Practice, ASM Press, Washington, DC, pp. 185–196.

    Google Scholar 

  • Graham, P.L. 3rd, Morel, A.S., Zhou, J., Wu, F., Della-Latta, P., Rubenstein, D., & Saiman, L. (2002). Epidemiology of methicillin-susceptible Staphylococcus aureus in the neonatal intensive care unit. Infect Control Hosp Epidemiol, 23, 677–682.

    Article  PubMed  Google Scholar 

  • Gupta, A., Della-Latta, P., Todd, B., San Gabriel, P., Haas, J., Wu, F., Rubenstein, D., & Saiman, L. (2004). Outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in a neonatal intensive care unit linked to artificial nails. Infect Control Hosp Epidemiol, 25, 210–215.

    Article  PubMed  Google Scholar 

  • Jarvis, W.R. (1995). Epidemiology of nosocomial fungal infections, with emphasis on Candida species. Clin Infect Dis, 20, 1526–1530.

    PubMed  CAS  Google Scholar 

  • Kazakova, S. V., Hageman, J.C., Matava, M., Srinivasan, A., Phelan, L., Garfinkel, B., Boo, T., McAllister, S., Anderson, J., Jensen, B., Dodson, D., Lonsway, D., McDougal, L.K., Arduino, M., Fraser,V.J., Killgore, G.,Tenover, F.C., Cody, S., & Jernigan, D.B. (2005).A clone of methicillin-resistant Staphylococcus aureus among professional football players. N Engl J Med, 3, 468–475.

    Article  Google Scholar 

  • Kluytmans, J., van Belkum, A., & Verbrugh, H. (1997). Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev, 10, 505–520.

    PubMed  CAS  Google Scholar 

  • Koort, J.M.K., Lukinmaa, S., Rantala, M., Unkila, E., & Siitonen, A. (2002). Technical improvement to prevent DNA degradation of enteric pathogens in pulsed field gel electrophoresis. J Clin Microbiol, 40, 3497–3498.

    Article  PubMed  CAS  Google Scholar 

  • Lopez-Canovas, L., Sanchez-Alonso, A., Higginson, D., Ariosa, C., Clark, H., & Riveron, A.M. (2003). Nonenzymatic protocol for Pseudomonas aeruginosa DNA preparation and rapid subtyping by mini pulsed-field gel electrophoresis. Electrophoresis, 24, 1152–1158.

    Article  PubMed  CAS  Google Scholar 

  • Maslow, J., & Mulligan, M.E. (1996). Epidemiologic typing systems. Infect Control Hosp Epidemiol, 17, 595–604.

    PubMed  CAS  Google Scholar 

  • Morel, A.S., Wu, F., Della-Latta, P., Cronquist, A., Rubenstein, D., & Saiman, L. (2002). Nosocomial transmission of methicillin-resistant Staphylococcus aureus from a mother to her preterm quadruplet infants. Am J Infect Control, 30, 170–173.

    Article  PubMed  Google Scholar 

  • Murchan, S., Kaufmann, M.E., Deplano, A., de Ryck, R., Struelens, M., Zinn, C.E., Fussing, V., Salmenlinna, S., Vuopio-Varkila, J., El Solh, N., Cuny, C., Witte, W., Tassios, P.T., Legakis, N., van Leeuwen, W., van Belkum, A., Vindel, A., Laconcha, I., Garaizar, J., Haeggman, S., Olsson-Liljequist, B., Ransjo, U., Coombes, G., & Cookson, B. (2003). Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spread of related strains. J Clin Microbiol, 41, 1574–1585.

    Article  PubMed  CAS  Google Scholar 

  • Okuma, K., Iwakawa, K., Turnidge, J.D., Grubb, W.B., Bell, J.M., O’Brien, F.G., Coombs, G. W., Pearman, J. W., Tenover, F.C., Kapi, M., Tiensasitorn, C., Ito, T., & Hiramatsu, K. (2002). Dissemination of new methicillin-resistant Staphylococcus aureus clones in the community. J Clin Microbiol, 40, 4289–4294.

    Article  PubMed  CAS  Google Scholar 

  • Pavlopoulou, I.D., Daikos, G.L., Alexandrou, H., Petridou, E., Pangalis, A., Theodoridou, M., & Syriopoulou, V.P. (2004). Carriage of Neisseria meningitidis by Greek children: risk factors and strain characteristics. Clin Microbiol Infect, 10, 137–142.

    Article  PubMed  CAS  Google Scholar 

  • Pfaller, M.A., Acar, J., Jones, R.N., Verhoef, J., Turnidge, J., & Sader, H.S. (2001). Integration of molecular characterization of microorganisms in a global antimicrobial resistance surveillance program. Clin Infect Dis, 32, S104–S113.

    Article  Google Scholar 

  • Romling, U., & Tummler, B. (2000). Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis. J Clin Microbiol, 38, 464–465.

    PubMed  CAS  Google Scholar 

  • Saiman, L., Ludington, E., Dawson, J.D., Patterson, J.E., Rangel-Frausto, S., Wiblin, R.T., Blumberg, H.M., Pfaller, M., Rinaldi, M., Edwards, J.E., Wenzel, R.P., & Jarvis, W. (2001). Risk factors for Candida species colonization of neonatal intensive care unit patients. Pediatr Infect Dis J, 20, 1119–1124.

    Article  PubMed  CAS  Google Scholar 

  • Saiman, L., Ludington, E., Pfaller, M., Rangel-Frausto, S., Wiblin, R.T., Dawson, J., Blumberg, H.M., Patterson, J.E., Rinaldi, M., Edwards, J.E., Wenzel, R.P., & Jarvis, W. (2000). Risk factors for candidemia in Neonatal Intensive Care Unit patients. The National Epidemiology of Mycosis Survey study group. Pediatr Infect Dis J, 19, 319–324.

    Article  PubMed  CAS  Google Scholar 

  • Saiman, L., O’Keefe, M., Graham, P.L. 3rd, Wu, F., Said-Salim, B., Kreiswirth, B., LaSala, A., Schlievert, P.M., & Della-Latta, P. (2003). Hospital transmission of communityacquired methicillin-resistant Staphylococcus aureus among postpartum women. Clin Infect Dis, 37, 1313–1319.

    Article  PubMed  Google Scholar 

  • Schwartz, D.C., & Cantor, C.R. (1984). Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell, 37, 67–75.

    Article  PubMed  CAS  Google Scholar 

  • Silbert, S., Boyken, L., Hollis, R.J., & Pfaller, M.A. (2003). Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619–621.

    Article  PubMed  CAS  Google Scholar 

  • Simpson, E. H. (1949). Measurement of diversity. Nature, 163, 688.

    Google Scholar 

  • Struelens, M. J. (1998). Molecular epidemiologic typing systems of baterial pathogens: current issues and perspectives. Memoirias do Instituto Oswaldo Cruz, Rio de Janeiro, 93, 581–585.

    CAS  Google Scholar 

  • Tenover, F.C., Arbeit, R.D., & Goering, R. V. (1997). How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Molecular Typing Working Group of the Society for Healthcare Epidemiology of America. Infect Control Hosp Epidemiol, 18, 426–439.

    Article  PubMed  CAS  Google Scholar 

  • Tenover, F.C., Arbeit, R.D., Goering, R. V., Mickelsen, P.A., Murray, B.E., Persing, D.H., & Swaminathan, B. (1995). Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol, 33, 2233–2239.

    PubMed  CAS  Google Scholar 

  • Turabelidze, D., Kotetishvili, M., Kreger, A., Morris, J.G. Jr., & Sulakvelidze, A. (2000). Improved pulsed-field gel electrophoresis for typing vancomycin-resistant enterococci. J Clin Microbiol, 38, 4242–4245.

    PubMed  CAS  Google Scholar 

  • Van der Ploeg, L.H., Schwartz, D.C., Cantor, C.R., & Borst, P. (1984). Antigenic variation in Trypanosoma brucei analyzed by electrophoretic separation of chromosome-sized DNA molecules. Cell, 37, 77–84.

    Article  PubMed  CAS  Google Scholar 

  • Wu, F., & Della-Latta, P. (2002). Molecular typing strategies. Semin Perinatol, 26, 357–366.

    Article  PubMed  Google Scholar 

Download references

Authors
  1. Fann Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Phyllis Della-Latta
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer

About this chapter

Cite this chapter

Wu, F., Della-Latta, P. (2006). Pulsed-Field Gel Electrophoresis. In: Advanced Techniques in Diagnostic Microbiology. Springer, Boston, MA. https://doi.org/10.1007/0-387-32892-0_9

Download citation

Publish with us

Policies and ethics

Search

Navigation