Detection of Haemonchus contortus on sheep farms increases using an enhanced sampling protocol combined with PCR based diagnostics

An enhanced sampling strategy for detection of gastrointestinal parasites of sheep based on faecal sampling covering approximately 10% of the animals in the flock was evaluated with focus on the major sheep pathogen Haemonchus contortus. We also compared traditional diagnostics based on faecal eggs counts (FEC) by microscopy with DNA detection on frozen faeces samples using a droplet digital (dd)PCR assay. The investigation was carried out in 2018 in 20 conventional and 19 organic sheep flocks in Sweden with between 70 and 250 production ewes. On 76 different sampling occasions a total of 810 individual faecal samples were collected. Samples were pooled in the laboratory into 270 triplets which were examined both by microscopy and a ddPCR assay. On most farms (95%) a minimum of three triplets were investigated, first from the ewes prior to turn-out and later from the lambs after they had been grazing for at least six weeks. Extra information about the Haemonchus status was provided on 48% of the 76 sampling occasions by including more triplets compared with the old sampling strategy applied in Sweden before 2015 based on two triplets per sampling occasion irrespective of flock size. At a farm level H. contortus was identified by microscopy in 22 (56%) of the 39 flocks and by ddPCR it was found in 28 (72%) flocks with the enhanced protocol. There was a substantial agreement between the two diagnostic tests (Cohens kappa = 0.70 ± 0.087). No significant differences in infection levels were observed between the two production systems (conventional and organic) irrespective of the diagnostic method used. However, samples from the ewes were more often Haemonchus positive than those from the lambs indicating that the level of parasite control was in general acceptable. Combined, our results show that Haemonchus infection is widespread throughout Sweden. In conclusion, we have validated a practical tool for sheep producers to assess Haemonchus infection with high precision.

Genetic variants in dyf-7 validated by droplet digital PCR are not drivers for ivermectin resistance in Haemonchus contortus

Resistance to ivermectin (IVM) in the nematode Haemonchus contortus in small ruminants is an increasing problem throughout the world. Access to molecular diagnostics will allow early detection of IVM resistance, which in turn can limit the spread of resistant isolates. One candidate gene which has recently been suggested as a marker for IVM resistance is that for dye-filling protein (dyf-7). In this study, we critically investigated the suitability of A141G and G153T single nucleotide polymorphisms (SNP) of dyf-7 as a marker in larval cultures collected from sheep farms in Sweden, involving several isolates for which resistance status had been characterised by the faecal egg count reduction test (FECRT). Initially, we designed dyf-7 primers from a worldwide collection of adult Haemonchus contortus DNA. With the sequence data, we created a haplotype network. We then optimised and used the same sets of primers and probes in a droplet digital PCR (ddPCR) assay for precise quantification of dyf-7 allele frequencies in pre- and post-anthelmintic treatment faecal larval cultures. The fractional abundance (FA) of the mutant SNP was within the range 7.8 and 31%. However, the FA was generally stable in samples collected from the same farms, even though they were obtained on different occasions up to 25 months apart. There was also no indication that the level of IVM resistance as measured by the faecal egg count reduction test was higher on farms with high FA. Furthermore, by comparing FA in samples from the same farms pre- and post-IVM treatment, we found no evidence of a correlation between dyf-7 and level of IVM resistance. Based on these results, dyf-7 is not a suitable marker for field testing of IVM resistance in H. contortus.