# Assessment of sponge sampling for real-time PCR detection of Cystoisospora suis from environmental and faecal samples from piglet-producing farms

## TL;DR

This study shows that sponges can effectively detect Cystoisospora suis in piglet farms as well as traditional fecal sampling when using real-time PCR.

## Contribution

The study introduces sponges as a viable alternative to fecal sampling for detecting C. suis in farm environments.

## Key findings

- Sponge sampling achieved a 67% positivity rate for C. suis detection, comparable to the 68% rate from fecal samples.
- Sponge sampling demonstrated 91.2% sensitivity and 84.8% specificity compared to fecal sampling as the gold standard.
- DNA mass from fecal samples was slightly higher than from sponges, with a moderate positive correlation (r = 0.51).

## Abstract

Cystoisospora suis (C. suis) infects piglets in their first week of life and can subsequently lead to diarrhoea and production losses. The detection of C. suis oocysts relies mostly on the collection of piglet faeces as sampling material and analysis through flotation and autofluorescence microscopy, which involves repeated sampling. The objective of the present study was to evaluate the use of sponges for environmental sampling for the detection of C. suis via real-time PCR and its suitability for surveillance programs applied on farms.

All farms included in the study were positive for C. suis according to qPCR, with positivity rates ranging from 20 to 100%. The frequency of positive cases was 68% for faecal samples and 67% for samples collected by sponges. The alignment between the different sampling protocols was 100% achieved at the farm level. In the case of the individual pair samples, a difference in 27 samples was observed (10.8%). Considering the faecal sampling strategy as the gold standard, the sensitivity of the sampling protocol with sponges was 91.2%, and the specificity was 84.8%. Compared with the sponge-collected samples, the faecal samples presented slightly greater DNA masses, with a correlation coefficient of r = 0.51, indicating a moderate positive relationship between the two sampling methods. An influence towards a higher DNA load with samples with a pasty and semiliquid consistency was observed, mainly in the case of the sponge technique.

Our results indicate that the collection of faecal samples at the litter or farm level and comparisons with environmental samples yield similar detection rates when sampling is combined with qPCR. From that perspective, the use of sponges for the detection of C. suis in organic material from the farrowing crate environment can be considered a good alternative to the more laborious and time-consuming collection of faecal samples.

The online version contains supplementary material available at 10.1186/s40813-025-00454-5.