Written and maintained by CASRAI Editorial Board
Last updated
Short answer
PFGE (pulsed-field gel electrophoresis) is a gel method that separates very large DNA fragments by repeatedly switching the direction of the electric field. Public-health labs used it for decades to fingerprint bacterial isolates; since 2019 PulseNet USA has used whole-genome sequencing (WGS) instead for its main pathogens.
Definition and scope
PFGE starts from intact bacterial chromosomes that are cut with a restriction endonuclease. In the Pennsylvania Salmonella outbreak investigation published in the Journal of Clinical Microbiology, cells were embedded in agarose plugs so the DNA stays unsheared, and the resulting fragments were “very large (approximately 20 kbp to 1,135 kbp)” (Sandt et al., 2006). Each lane on the finished gel is one isolate’s fingerprint, and analysts mark the bands by molecular weight (Tolar et al., 2019).
Within the lab-techniques cluster, PFGE sits beside conventional gel electrophoresis and the agarose gel basics that most benches run daily. Those methods use a single constant field; PFGE is the variant built for fragments too large for it.
How PFGE works in practice
Bio-Rad’s technology page describes the defining feature: PFGE “resolves DNA by alternating the electrical field between spatially distinct pairs of electrodes,” and the first field is switched to the second “according to the run specifications.” The manufacturer states the technique separates DNA up to roughly 10 Mb. Sandt et al. note that this needs a specialized power supply and chamber to produce the alternating fields.
After the run, isolates with indistinguishable patterns are grouped. Patterns are compared against a universal size standard, and gel images are normalized in analysis software (BioNumerics in the Pennsylvania study). That study also reports that assigning bands is “time-consuming and somewhat subjective,” and that the software’s suggestions “must be evaluated and fine-tuned manually.”
Types and related concepts
PFGE system types
Bio-Rad’s technology page describes these instrument approaches:
- CHEF (clamped homogeneous electrical field).
- PACE, with a selectable pulsing angle.
- CHEF-DR, which regulates each of 24 electrodes.
- FIGE / AFIGE (field inversion gel electrophoresis), described by the vendor as allowing rapid separation.
PFGE compared with WGS and ordinary agarose gels
| Method | What it reads | Sourced detail |
|---|---|---|
| Conventional agarose gel | Fragment size under a constant field | Bio-Rad contrasts its roughly 20 kb range with PFGE’s ~10 Mb ceiling |
| PFGE | Restriction-fragment pattern of the whole chromosome | Fragments about 20 to 1,135 kbp in the Sandt study; band marking subjective |
| Whole-genome sequencing | Sequence of the isolate | Primary subtyping tool at PulseNet USA for Listeria, Salmonella, E. coli, Shigella and Campylobacter from 2019 |
For the sequencing side, see CASRAI’s guides on Sanger sequencing and sequencing depth and breadth of coverage.
Where PFGE matters for labs and supply decisions
Why surveillance moved on
Tolar et al. (Foodborne Pathogens and Disease, 2019) describe the PulseNet USA transition. A WGS pilot began in 2013; WGS has been required for Listeria since 2018; and the move to WGS as the primary subtyping tool was completed in 2019 for Listeria, Salmonella, E. coli, Shigella and Campylobacter, with Vibrio, Yersinia and Cronobacter to follow. The paper lists the PFGE limits behind that shift:
- Not all bacterial strains produce PFGE patterns when cut with standard restriction enzymes.
- In clonal organisms (for example Salmonella Enteritidis) PFGE may not separate outbreak isolates from background.
- Closely related isolates can show different patterns.
- Marking pattern bands is subjective and bands were at times not marked the same way across laboratories.
What a lab needs to run it
A PFGE capability involves four things: a dedicated chamber and switching power supply (Sandt; Bio-Rad’s system types), agarose-embedded DNA so chromosomes stay intact, restriction endonucleases, and image-analysis software that normalizes bands to a size standard. A comparable restriction enzyme digest on short DNA needs none of the field-switching hardware, which is the practical dividing line between PFGE and routine gel work.
Common misunderstandings
- “PFGE is just a slower agarose gel.” The alternating field, not the run length, is what defines it, and it is what lets fragments in the hundreds of kilobases resolve (Bio-Rad; Sandt).
- “PFGE sequences the genome.” It does not. It produces a band fingerprint of restriction fragments; sequencing is the method that replaced it in PulseNet USA.
- “Identical patterns always mean one outbreak.” For clonal organisms Tolar et al. report PFGE may fail to separate outbreak from background isolates.
- “Every strain can be typed.” Some strains do not produce patterns with standard enzymes (Tolar et al.).
FAQ
What does PFGE stand for?
Pulsed-field gel electrophoresis: gel electrophoresis in which the electric field is alternated between electrode pairs to separate very large DNA fragments.
What size of DNA can PFGE separate?
Bio-Rad states up to roughly 10 Mb. In the Pennsylvania Salmonella study, restriction fragments ran from about 20 to 1,135 kbp.
Is PFGE still used?
PulseNet USA completed its transition to WGS as the primary subtyping tool in 2019 for five major pathogens, with three more to follow, so PFGE is no longer the primary tool there. The technique itself and its instrument families (CHEF, PACE, FIGE) remain described by manufacturers.
PFGE vs WGS: what is the difference?
PFGE compares restriction-fragment band patterns, with subjective band marking. WGS compares sequence data and is what PulseNet USA adopted in its place.
Sources
- Tolar B et al. “An Overview of PulseNet USA Databases.” Foodborne Pathogens and Disease 2019;16(7):457-462. pmc.ncbi.nlm.nih.gov/articles/PMC6653802 (checked 2026-10-29).
- Sandt CH et al. Journal of Clinical Microbiology 2006;44(9):3208-3212. pmc.ncbi.nlm.nih.gov/articles/PMC1594743 (checked 2026-10-29).
- Bio-Rad, pulsed field gel electrophoresis technology page. bio-rad.com (checked 2026-10-29).
