Rumen fluke are parasitic trematodes that affect domestic and wild ruminants across a wide range of countries and habitats. There are 6 major genera of rumen fluke and over 70 recognized species. Accurate species identification is important to investigate the epidemiology, pathophysiology and economic impact of rumen fluke species but paramphistomes are morphologically plastic, which has resulted in numerous instances of misclassification. Here, we present a universal approach to molecular identification of rumen fluke species, including different life-cycle stages (eggs, juvenile and mature fluke) and sample preservation methods (fresh, ethanol- or formalin-fixed, and paraffin wax-embedded). Among 387 specimens from 173 animals belonging to 10 host species and originating from 14 countries on 5 continents, 10 rumen fluke species were identified based on ITS-2 intergenic spacer sequencing, including members of the genera Calicophoron, Cotylophoron, Fischeroedius, Gastrothylax, Orthocoelium, and Paramphistomum. Pairwise comparison of ITS-2 sequences from this study and GenBank showed >98.5% homology for 80% of intra-species comparisons and <98.5% homology for 97% of inter-species comparisons, suggesting that some sequence data may have been entered into public repositories with incorrect species attribution based on morphological analysis. We propose that ITS-2 sequencing could be used as a universal tool for rumen fluke identification across host and parasite species from diverse technical and geographical origins and form the basis of an international reference database for accurate species identification.

Rumen fluke (RF) are trematode parasites that have increased in prevalence within European ruminant livestock since the 1990s. Morbidity and mortality can result from the development of juvenile flukes in the duodenum, however, evidence for significant impacts of adult fluke in the rumen of the final host is equivocal. The presence of rumen fluke in Scotland had not previously been quantified, so the purpose of this study was to use historical coprological data collected between 2008 and 2018 at the School of Veterinary Medicine in Glasgow to evaluate the frequency of rumen fluke infection and to compare this with the presence of liver fluke. This analysis showed evidence of adult rumen fluke in 6.6% of samples submitted, with a substantial and significant increase in positive diagnoses from 2016, following which positive rumen fluke diagnoses equaled or slightly outnumbered those of liver fluke. A prospective post-mortem examination study was also carried out to determine the presence of rumen and liver fluke in cattle and sheep, to quantify adult rumen fluke burdens and to assess any pathological changes in the reticulorumen and proximal duodenum associated with infection. The presence of rumen fluke in post-mortem cases was 26.9% (n = 18/67), the majority (66.7%, n = 12/18) with burdens of less than 100 adult rumen flukes. There was no significant difference in mean ruminal papillar density and length in animals with and without adult rumen fluke and no significant gross pathology was observed in the rumen or reticulum. Examination of animals with adult rumen fluke provided no evidence of any consistent associations with acute or chronic inflammatory changes in the duodenum. All rumen fluke collected at necropsy were identified by PCR and sequencing as Calicophoron daubneyi.