Abstract
In the faecal egg count reduction test, visual identification of larvae cultured from faeces enables the egg counts to be apportioned to species/genera, resulting in a more accurate test. However, morphology cannot reliably differentiate some species meaning that, in some cases, efficacy can only be estimated at the genus or species-complex level. We investigated the benefits of identifying larvae to species using DNA to determine how often this would alter the diagnosis of resistance and whether increasing the number of larvae identified would alter the repeatability of an efficacy estimate. Data on faecal nematode egg counts and the corresponding larval species mixes were acquired from tests conducted on commercial sheep farms. The proportion of each species present in faecal culture was determined using DNA. Efficacy was then compared for individual species and for those genera/species complexes which cannot reliably be differentiated visually. The proportion of each species present was subsequently resampled 10,000 times (repeated random sampling) and efficacy recalculated to produce the median efficacy, along with the 5 % and 95 % simulation percentiles. Subsequently, the number of larvae sampled to determine the species mix in each sample was varied from 50 to 6400 and the process repeated. Of 152 comparisons of efficacy, 25 % of cases where genus-level identification resulted in a finding of 'susceptible' for that category, species-level identification returned at least one diagnosis of 'resistant' i.e., genus-level identification resulted in a 25 % false negative diagnosis. When the number of larvae sampled for species identification was low (<400) variation in efficacy estimates was high, however, as sample size increased the confidence interval around the efficacy estimate decreased. The results indicate that identifying large numbers of larvae to species using DNA has the potential to increase the accuracy and confidence in efficacy estimates achieved using the faecal egg count reduction test.