Pulsed-field gel electrophoresis (PFGE): A review of the “gold standard” for bacteria typing and current alternatives

• Published in: Infection, genetics and evolution Vol. 74; p. 103935
• Main Authors: Neoh, Hui-min, Tan, Xin-Ee, Sapri, Hassriana Fazilla, Tan, Toh Leong
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2019
• Subjects: Bacteria - classification; Bacteria - genetics; Bacteria typing; Bacterial Typing Techniques - methods; Electrophoresis, Gel, Pulsed-Field; Food Microbiology; Phylogeny; Pulsed-field gel electrophoresis (PFGE); Whole Genome Sequencing; Bacteria typing; Pulsed-field gel electrophoresis (PFGE)
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2019.103935

Pulsed-field gel electrophoresis (PFGE) is considered the “gold standard” for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come. •PFGE is the “gold standard” for bacteria typing; standardized protocols are available.•PFGE is useful for phylogenetic studies, infection control and food safety monitoring.•PCR-based typing such as rep-PCR, ERIC-PCR and MLVA can be alternatives for PFGE.•Some laboratories are transitioning towards whole genome sequencing-based typing.•PFGE remains important for small hospitals and laboratories with limited resources.