Comparison of whole-genome sequencing and pulsed field gel electrophoresis for characterizing relationships in Mannheimia haemolytica

Abstract

It has long been presumed that cattle developing BRD tend to become sick from their own native strains of Mannheimia haemolytica. Previous work by others has demonstrated that the diversity of Mannheimia haemolytica, as evaluated by PFGE, within a pen of cattle remains high during BRD outbreaks. Prior to the development of whole genome sequencing (WGS), pulsed field gel electrophoresis (PFGE) had been considered the gold standard for characterizing outbreaks of bacterial disease. Recently, many studies from the human literature have raised question regarding the accuracy of PFGE as WGS has become more widely implemented. Studies investigating Acinetobacter baumanii, Clostridium difficile, and vancomycin resistant Enterococci outbreaks in hospitals have shown WGS to have superior discernment and more accurately classify strains when compared to PFGE. Considering the superiority of WGS in characterizing outbreaks in all of these species, if may be that relationships inferred in Mannheimia haemolytica based on PFGE could be inaccurate. It is therefore our goal to compare the discernment ability of PFGE and WGS for Mannheimia haemolytica isolates collected from beef cattle.