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Research Summary - 2

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

Date/Time: 9/13/2019    09:00
Author: Emily  Snyder
Clinic: University of Georgia
City, State, ZIP: Athens, GA  30602

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

E.R. Snyder, DVM, MFAM 1 ; C.M. Logue, PhD 2 ; B.C.Credille, DVM, PhD, DACVIM 1 ;
1Food Animal Health and Management, Department of Population Health, University of Georgia, Athens, GA, 30602
2Department of Microbiology, University of Georgia, Athens, GA, 30602

Introduction:

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.

Materials and Methods:

A total of 48 Mannheimia haemolytica isolates collected from lightweight beef cattle that had been collected as part of another study were submitted for PFGE. An identity cutpoint of 90% was used to cluster the isolates, and a dendrogram was generated. Whole genome sequences of the same 48 isolates that had been sequenced as part of another study were submitted to the CSI Phylogeny web interface for alignment. The resulting alignment file was used to create a maximum likelihood tree using RAxML version 8.2.11 in Geneious, using a GTR GAMMA nucleotide model and running 1,000 bootstrap replicates.

Results:

The tree produced by PFGE found the isolates falling into 11 different clusters. The tree produced by WGS placed the isolates into a total of 4 different clusters. Multiple isolates that had been grouped together by WGS were not grouped together by PFGE.

Significance:

As has been seen in the human literature, the results of this study suggest that PFGE may not accurately classify Mannheimia haemolytica isolates when compared to the results from WGS. This study furthermore suggests that PFGE may imply greater diversity in isolates than is actually present based on WGS.


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