A high throughput deep amplicon sequencing method to show the emergence and spread of Calicophoron daubneyi rumen fluke infection in United Kingdom cattle herds

The prevalence of C. daubneyi infection in the United Kingdom has increased, but despite the potential for rumen flukes to cause production loss in ruminant livestock, understanding of their emergence and spread is poor. Here we describe the development of a method to explore the multiplicity of C. daubneyi infection and patterns of the parasite's emergence and spread, based on Illumina MiSeq deep sequencing of meta barcoded amplicons of a fragment of the cytochrome c oxidase subunit I (mt-COX-1) locus. Our results show high levels of genetic diversity in 32 C. daubneyi populations derived from finished prime cattle consigned to slaughter from northern United Kingdom. The results are consistent with a single introduction of C. daubneyi infection to some of the farms where the cattle had been grazed during their lifetime and multiple introductions to most. The results illustrate the impact of high levels of animal movements in the United Kingdom, whereby multiple common mt-COX-1 haplotypes were identified in 26 populations in the absence of geographical clustering of clades. This has implications for the adaptability of environmental and intermediate host stages of the parasite to changing climatic and animal management conditions, or of parasitic stages to exposure to anthelmintic drugs; potentially allowing for greater pathogenicity, or the development of anthelmintic resistance, respectively.