Small Ruminant Gastrointestinal Parasite Diagnosis (PCR and FEC)

The specific diagnosis of gastrointestinal parasitism in small ruminants is time consuming by routine coprological methods and only provides limited sensitivity and specificity. Faecal worm egg counts and differential larval counts are only an approximate guide to the parasite burden. Egg counts are also influenced by factors as faecal consistency and bulk (diarrhoea reduces the egg count), host resistance, stage of pregnancy, effects of lactation and whether the worm burden consists of sexually mature parasites.

Over several years of research scientists at the University of Melbourne in collaboration with AusDiagnostics have developed a novel approach for the specific diagnosis of most important nematode species/genera infecting small ruminants, including Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus spp., Chabertia ovina and Oesophagostomum venulosum.

This novel molecular diagnostic approach is available through the diagnostic service of Gribbles Veterinary Pathology.

The service includes the following:

  • Parasitological diagnosis of small ruminant faecal samples including a pooled faecal egg count (FEC) and the molecular (PCR-based) identification of five key species/genera.
  • Estimates for the contribution of different species to the observed FEC (given as %).


Small ruminants


2 - 4g individual or pooled faecal samples


Sterile pot

Collection protocol:

  • If requiring bulk testing, select groups of 10 - 20 animals to represent the range of body condition scores of the flock. It is best to do one or more bulk tests per group of animals within a paddock e.g. young stock, males and females. Try to avoid selecting animals at the tail end of the group as this may bias the interpretation.
  • Collect individual faecal samples directly from the rectum of each animal (not from the ground unless freshly passed in a clean yard).
    • Place each sample in a separate pot labelled with the appropriate identification of the property and the individual/group of animals. Sampling containers should be filled to top if possible:
    • 4 g = optimal amount of sample for the assay diagnostic performance
    • 2 - 3.5 g = still able to produce results; however the same performance as with 4 g cannot be guaranteed
    • <2 g = should be excluded from analysis
  • Fill out the submission form appropriately, requesting a gastrointestinal nematode test by PCR (Ovine).

Special handling/shipping requirements:

Samples should be submitted fresh (within 12 hours is preferred). If submission is going to be delayed, the faecal material can be refrigerated up to 7 days.



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Roeber F, Jex AR, Campbell AJD, Campbell BE, Anderson GA, Gasser RB: Evaluation and application of a molecular method to assess the composition of strongylid nematode populations in sheep with naturally acquired infections. Infection, Genetics and Evolution 2011, 11(5):849-854.

Roeber F, Larsen JWA, Anderson N, Campbell AJD, Anderson GA, Gasser RB, Jex AR A Molecular Diagnostic Tool to Replace Larval Culture in Conventional Faecal Egg Count Reduction Testing in Sheep PLoS ONE 2012a, 7(5):e37327.

Roeber F, Jex A, Campbell AJD, Nielsen R, Anderson G, Stanley K, Gasser R: Establishment of a robotic, high-throughput platform for the specific diagnosis of gastrointestinal nematode infections in sheep. Int J Parasitol2012b, 42(13-14):1151-1158.

Roeber F, Jex AR, Gasser RB: Comparative evaluation of two DNA isolation techniques for PCR-based diagnosis of gastrointestinal nematode infections in sheep. Mol Cell Probes 2013, 27(3–4):153-157.