Rapid identification and differentiation of agricultural faecal contamination sources using multiplex PCR

Aims: To develop a quick, easy-to-use, robust and sensitive multiplex PCR assay to detect common sources of agricultural faecal contamination using a combination of bacterial and eukaryote-specific PCR targets. Method and Results: A novel multiplex PCR method was developed that utilizes primers specific for a conserved region of the eukaryote cytochrome-B gene as well as a universal 16S rRNA and the E. coli-specific uidA gene. This multiplex PCR assay was capable of identifying faecal amendments from pig, sheep, cow and goat sources in 24/30 (80%) of amended water samples. Conclusions: The method was capable of accurately identifying common agricultural sources. Significance and Impact of the study: The procedure described here is simple, rapid (< 5 h) and can be used as a first step in microbial source tracking studies, particularly where agricultural faecal contamination is suspected.