1a. Objectives (from AD-416):
To discover single nucleotide polymorphisms (SNPs) that identify and classify bacterial pathogen genetic subtypes into their clinically important and biologically relevant groups.
1b. Approach (from AD-416):
The genomes of epidemiologically unlinked bacterial pathogen strains originating from either clinically ill or asymptomatic cattle will be sequenced and mapped to finished reference genomes. Thousands of SNP differences will likely be identified among these strains and used to produce a phylogenetic tree of pathogen genetic subtypes. The SNPs will be evaluated in silico for their utility in distinguishing and classifying all of the genetic subtypes discovered in this study. BioLog data will be used to characterize the subtypes and calibrate the tree. Clades of the tree that represent related subtypes will be tested for an association with pathogenicity.
3. Progress Report:
Bovine Respiratory Disease Complex (BRDC) is a serious health and economic problem that costs the United States cattle industry over a billion dollars annually. Bacteria called Mannheimia haemolytica cause the predominant pneumonia associated with BRDC. The primary goal of this project is to discover key DNA variation that can be used in a diagnostic test to identify and classify M. haemolytica genetic subtypes. Accordingly, in the first year of this project, a large collection of over three hundred M. haemolytica strains was acquired from a collaborator. The strains were isolated from diseased cattle throughout the United States and Canada, and thus represent a deep sampling of M. haemolytica in North America. Since their acquisition, all of the strains in the collection have been subjected to biochemical tests to confirm their identity as M. haemolytica and to characterize their diversity. Whole genome sequencing of all the isolates in this collection is currently underway for the discovery of DNA variation. The genomes of 24 isolates have been sequenced as of the writing of this report with the rest of the collection soon to follow.