Using genetic analysis to determine the distribution, prevalence and diversity of Eimeria species in pest rabbits (Oryctolagus cuniculus) in Australia.

To genetically assess the Australian distribution and frequency of Eimeria species in wild rabbits, with a primary focus on Eimeria intestinalis and Eimeria flavescens as possible additional agents of rabbit biocontrol, the distal colon and faecal samples from wild rabbits sourced from 26 Australian locations with mean annual rainfalls of between 252 mm and 925 mm were analysed using amplicon sequencing of the ITS1 region. Contrary to previous microscopy studies which had only detected E. flavescens on mainland Australia at Wellstead in south-west Western Australia, we detected this species at all 23 effectively sampled sites. The more pathogenic E. intestinalis was only found at 52.2% of sites. Three unique Eimeria genotypes were detected that did not align to the 11 published sequences using a pairwise-match threshold of 90%, and may represent unsequenced known species or novel species. One genotype we termed E. Au19SH and was detected at 20 sites, E. Au19CO was detected at eight sites, and E. Au19CN was detected in one rabbit at Crows Nest (Qld). Site diversity ranged from only five Eimeria species at Boboyan (ACT) to 13 unique sequences at Cargo (NSW). Eimeria diversity in individual rabbits ranged from 11 unique sequences in a rabbit at Wellstead (WA) and a rabbit at Cargo (NSW), to one in 17 rabbits and zero in six rabbits. The three rabbit age classes averaged 4.3 Eimeria species per rabbit. No relationship was found between the number of Eimeria species detected and mean annual rainfall. As Eimeria species were found to be fairly ubiquitous at most sites they appear to be an unlikely additional candidate to assist the control of pest rabbits in Australia.