Within Australia, each species of Eimeria may be represented by one large inter-breeding population, where outbreak strains sweep the country each year like a flu epidemic. Alternatively, strains may be spatially diversified, with geographic barriers helping to maintain their unique genetics.

Using neutral genetic markers (DNA markers not under selection pressure), this research will provide information about how strains relate to one another. Understanding the relatedness of strains will indicate how Australian strains of Eimeria have spread over time through the continent.

Dr Morgan explains her interest in this field of study: “I find molecular parasitology rewarding because it allows me to study organisms that have traditionally been difficult to work with because they are microscopic, visually cryptic and/or have complex life cycles. Not only can molecular technology be used for diagnostic purposes, it can also reveal the secrets of disease origin and spread.”

To date, the project has observed some quite unexpected discoveries. One of these has been the high incidence around Australia of the identified, but uncharacterised, genetic species OTU-Y.

“This genetic species occurs in every state and territory, and in backyard flocks it is the second most prevalent species (in 39 per cent of infected samples) after Eimeria mitis (in 46 per cent of infected samples). In commercial flocks, where coccidiostats are in common use, E. acervulina is the most prevalent species (in 76 per cent of infected samples) but OTU-Y is still present (in six per cent of infected samples). Field screening shows that Eimeria species are widespread, however, preliminary data suggests that within species population structure exists, as strain prevalence varies from state to state” said Dr Morgan.

Strain differences could influence how well a flock responds to treatment. An understanding of strain variability will also assist in vaccine improvement, as challenge trials can be conducted between distantly related strains to ensure maximum flock protection is attained. As Dr Morgan expounds: “being able to distinguish live vaccine from wild strains of Eimeria will enable accurate testing of outbreaks in vaccinated flocks. If an outbreak is occurring in the presence of vaccine strains, then a breakthrough has occurred. In contrast, if only the outbreak strain is found (i.e. no vaccine strains) then there may be a problem with the vaccine batch or in the vaccination procedure.”

This project has involved collecting and screening a lot of chicken faeces from around the country. Dr Morgan is grateful for the assistance and says: “I would like to take this opportunity to thank all of the industry and backyard chook owners who have kindly offered their time and samples to assist us with this research.”