Fowl cholera caused by Pasteurella multocida continues to be a problem in meat chicken breeder operations and has emerged in organic meat chicken and free-range layer production systems as well.
Lipopolysaccharide is one of the most important immunogenic virulence factors of P. multocida. Recent works have demonstrated that killed vaccines give protection only against strains with identical or nearly identical lipopolysaccharide (LPS) structures. As well, P. multocida strains of LPS genotype 3, identified by PCR, can have a range of truncated lipopolysaccharides.
Here we use whole genome sequencing and phylogenomic analysis to investigate isolate relatedness during outbreaks of fowl cholera over the years within two free-range poultry farms. A total of 125 P. multocida isolates were collected from two unrelated farms, one organic meat chicken and one free-range layer farm during cholera outbreaks. Whole genome sequencing data has been also used to predict the LPS outer core biosynthesis locus type and the multi locus sequence typing (MLST) of the isolates.
In silico LPS typing identified that the majority of isolates on both farms were carrying LPS type 3 with a small number of isolates on the meat chicken farm characterised as carrying LPS type 1. Sequence comparisons revealed that LPS outer core biosynthesis locus of the isolates carrying LPS type 1 were highly conserved. In contrast, the LPS locus of type 3 isolates were found to be highly diverse, which complicates selection of an appropriate and effective vaccine.
Core genome SNP tree demonstrated that isolates within each outbreak are highly related to each other. Moreover, different clones of P. multocida have been responsible for fowl cholera outbreaks over time. We also demonstrated that different clones of P. multocida have the capacity of carrying LPS type 3. The capacity of using genomics data to predict the structure of LPS type 3 will be further discussed
Our study clearly demonstrates that in silico LPS and MLST typing are suitable substitution for older genomics methods.
This project is co-funded by AgriFutures Australia and Australian Eggs.