Pasteurella multocida is a commensal organism that can cause disease in a wide range of animal species such as mammals including marsupials and marine mammals, as well as different avian hosts. 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.
Here we use whole genome sequencing (WGS) and phylogenomic analysis to investigate isolate relatedness during outbreaks of fowl cholera over the years within different free-range poultry farms. Whole genome sequencing data has been also used for in silico typing of lipopolysaccharide (LPS) outer core biosynthesis locus and for multi locus sequence typing (MLST) of the isolates. As well, P. multocida isolates associated with pneumonia and/or septicaemia in other animal species such as in-captive Australian marsupials and fur seals were compared to the fowl cholera isolates to have a better understanding of epidemiology of this organism in association with different hosts.
In silico LPS typing identified that the majority of the isolates associated with fowl cholera and seal and marsupial pneumonia harbour LPS type 3. However, isolates obtained in association with oropharyngeal disease or septicaemia in in-captive Australian marsupials appeared to carry LPS type 4. Subtypes of LPS type 3 could also be identified using WGS data. We also demonstrated that different clones of P. multocida have the capacity of carrying LPS type 3.
In conclusion, our study clearly demonstrates that in silico LPS and MLST typing are suitable methods in place of PCR based methods. As well, genomic analysis provides clear insights in terms of linkage of isolate within and between outbreaks and links across different host species. The identified diversity within isolates that carry LPS type 3 complicates the selection of appropriate vaccine strains.