E. W. Brown, C. E. Keys, CFSAN, FDA, College Park, MD
The importance of PFGE (pulsed-field gel electrophoresis) as a strain discriminator is well established, however, it remains unclear in which instances PFGE-based strain clusterings reiterate evolutionary history. This question is of paramount importance when attempting to trace origin among outbreak strains. Here, phylogenetic utility of PFGE is assessed among three populations of Salmonella enterica—the SARA, SARB, and SARC reference collections, each representing a distinct level of taxonomic diversity. Comparisons of resultant PFGE trees with MLEE (multi-locus enzyme electrophoresis) and mdh (malate dehydrogenase) gene phylogenies, both of which reflect the evolutionary relationships of Salmonella strains, revealed substantial incongruence for all three strain collections indicating that PFGE phylogenies deviate considerably from actual strain evolution. For example, SARC sibling strains representing four of the eight S. enterica subspecies were broken into disparate locales on the PFGE tree. In the PFGE SARB tree, representing S. enterica subspecies I, five of six clades comprised strains from at least two different MLEE and mdh lineages. The PFGE tree representing the highly homogeneous SARA strains, consisting of S. Typhimurium and its four closest serovars, also appeared evolutionarily obscured. Four of five clades retained strains from diverged MLEE lineages while three clades comprised strains from diverse mdh lineages. These data suggest that, in Salmonella, the reconstitution of evolutionarily meaningful strain groupings may be a largely intangible task for PFGE. Moreover, our findings underscore previously noted pitfalls in using single-enzyme PFGE analysis to obtain accurate genetic relationships. Currently, we are exploring combinations of enzymes for improved phylogenetic accuracy.