Toward Standardization of Diagnostic PCR Testing of Fecal Samples: Lessons from the Detection of Salmonellae in Pigs

Abstract

Why fecal samples? The International Organization for Standardization and the European Committee for Standard- ization have recently decided to include the standardization of fecal testing in their agenda. The aim is to prepare documents describing standardized protocols for the detection of epide- miologically important zoonotic agents, which can often be found in low numbers in fecal samples in food production animals. The effort is to provide standard protocols for primary samples as part of the farm-to-fork approach. Samples taken from the primary production herds have been rather neglected in the standardization efforts compared to food or clinical samples. The work will include both conventional and PCR-based methods in order to improve the detection limit, particularly in subclinically infected herds. The present review with recom- mendations is the first of three reviews which will pave the way for standard protocols, facilitating the comparison of epidemi- ological data and providing quantitative methods for microbi- ological risk assessments. are the main sample matrix taken for Salmonella monitoring programs in swine herds, since pigs shed the pathogen through feces, which can be easily collected from individual animals. The detection of Salmonella in feces is done mainly by using traditional bacteriological methods, despite the availability of rapid, cost-effective, and reliable PCR-based methods devel- oped within the last few years. Here, an automated PCR test- ing system for monitoring Salmonella in swine herds could screen thousands of feces samples in a short period to obtain substantial data for qualitative and quantitative risk assess- ments. The expected high proportion of negative samples could then be discarded, whereas the positive samples could be cultured for the isolation of strains useful for further epidemi- ological studies. However, although the technology is available, such a system has not yet been implemented. The main reason for not using PCR testing more widely could be the lack of standardized protocols directed towards the detection and quantification of pathogens in such a difficult material as feces. Although substantial PCR standardization efforts have been done on food samples (26), important primary samples such as feed and feces have not yet received sufficient attention.