A rapid molecular approach to determining the occurrence of pathogen indicators in compost

Abstract

An accurate method for enumerating pathogen indicators, such as Escherichia coli (E. coli), and Salmonella spp. is important for assessing the safety of compost samples. This study aimed to determine the occurrence of pathogen indicators in compost samples by using a molecular approach known as Polymerase Chain Reaction (PCR). The DNA sample was extracted from sewage sludge compost. The specificity of the probes and primers at the species level were verified by performing NCBI-BLAST2 (Basic Local Alignment Search Tool). Primers that target the gadAB gene for E.coli and invA gene for Salmonella spp. were selected which produce fragment lengths around 670bp and 285bp respectively. The primers were tested against bacterial cultures of both species and produced a strong signal band of the expected fragment length. It provided results within 6 hours which is relatively rapid compared to conventional culturing techniques. The other advantages of PCR are shown to be its high sensitivity, and high specificity.