Pulsed Field Gel Electrophoresis (PFGE) was selected by PulseNet as the primary genotyping methodology back in the mid 1990's. As a robust and reliable technique it has surpassed all expectations, and remains today the primary method for network participants. This page includes PFGE protocols, PulseNet under the Microscope newsletters (currently covering Image acquisition, agaroses for PFGE, and DNA stains), a link to YouTube videos explaining PFGE (in Spanish only) useful information on the Salmonella serotype Braenderup (H9812) universal standard strain, and general information on equipment needed for PFGE.
The following information provides the standard laboratory protocols for molecular subtyping of the pathogens under surveillance by PulseNet laboratories. Clicking on the name or photograph of an organism will link you to the Adobe Acrobat version of the PulseNet protocol for that organism.
Updated March 2013, PDF 204 KB
March 2010, PDF 833 KB
Escherichia coli (O157:H7 and non O157), Salmonella, Shigella sonnei and Shigella flexneri
Updated March 2013, PDF 173 KB
Updated March 2013, PDF 225 KB
Vibrio cholerae and Vibrio parahemolyticus [PDF, 163 KB]
Updated April 2015, PDF 163 KB
April 2006, PDF 210 KB
A series of updates and hints from the PulseNet method development laboratory.
Capturing a Gel and Adjusting the Settings for Analysis
DNA stains for agarose gels (ethidium bromide, SYBR Safe, SYBR Gold, GelRed)
A comparison of agaroses for PFGE (Seakem Gold, Agarose III, Megabase, PFGE Agarose).
PulseNet Latin America have produced a series of videos explaining PFGE. These have been uploaded to YouTube(external link) where they are accessible to all - but at this stage only in Spanish!(external link)
For PFGE normalization and accurate comparison of gel images require the use of a well-characterized size standard in at least three lanes of each gel. PulseNet International has adopted a strain of Salmonella serotype Braenderup (H9812) restricted with XbaI was selected as a "universal" standard strain because of its even distribution of bands over the entire range of band sizes normally seen in the foodborne pathogens tracked by PulseNet. This strain was found to have a stable PFGE pattern upon subculture and was susceptible to antimicrobial agents commonly used to treat serious Salmonella infections.
This strain has been deposited with the American Type Culture Collection (BAA-664)(external link) to make it available for other laboratories to use.
Approximate band sizes in kilobases of the Salmonella serotype Braenderup reference standard (H9812) restricted with XbaI and run under the PulseNet standardized electrophoresis conditions specific for each organism.
Details of the development of this standard have been described in the following paper:
Hunter SB, Vauterin P, Lambert-Fair MA, Van Duyne MS, Kubota K, Graves L, Wrigley D, Barrett T, Ribot E.(external link)
Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard.
J Clin Microbiol. 2005 Mar;43(3):1045-50.
PulseNet PFGE protocols have been developed and validated for use on Bio-Rad CHEF Mapper XA System or CHEF-DR III System.
A list of equipment and supplies needed for the molecular subtyping of foodborne bacterial pathogens by PulseNet´s Standardized PFGE Protocols can be downloaded here.
Costs given are approximate, are in US$, and were correct as of January 10, 2007
Use of trade names and commercial sources is for identification only and does not imply endorsement by CDC, the U.S. Department of Health and Human Services, or any PulseNet International participant.