Diagnosis of parasite infections in faeces has traditionally relied on microscopy of concentrates and stained permanent faecal smears. This method of diagnosis however has a number of limitations as it depends on the subjective identification of parasites based on morphological features, sufficient parasite numbers for detection, and requires experienced staff to interpret the smears, resulting in an overall low sensitivity. While the morphologies of Giardia intestinalis trophozoites and cysts are sufficiently characteristic to allow distinction from other parasites, specificity of microscopy can also be a limiting factor. For example, pathogenic Entamoeba histolytica cannot be distinguished from the non-pathogenic E dispar. Additional techniques such as PCR or ELISA must therefore be used to differentiate between these species. Finally microscopy, particularly for detection of Dientamoeba fragilis, is reliant on prompt fixation of the faeces as the trophozoites degenerate within a few hours of being passed making it difficult to detect the characteristic structures required to make the identification.

This presentation outlines the approach to introducing molecular assays for detection of E histolytica, G intestinalis, Cryptosporidium spps and D fragilis in faeces into a routine diagnostic laboratory. A key requirement was optimisation of an automated extraction procedure permitting high throughput testing of ~400-500 samples/week. PCR detection was at least 2-5x more sensitive than microscopy, specific and reproducible. In addition, PCR did not require rapid fixation of samples, reduced the turnaround time and resulted in new insights into the epidemiology of faecal parasite infections in a developed country.