Scientists have developed a new method for detecting fecal contamination in water using human viral DNA, which can help improve the safety of water sources while also allowing for microbial source tracking of contamination.

Traditional tests for fecal contamination in water rely on culturing fecal indicator bacteria. The new method, developed by researchers from Chungnam National University and Gyeongsang National University, offers advantages over the traditional method in that it can detect low-level contamination and determine the source of contamination. The new method is based in microbial source tracking (MST) technology, which involves the detection of biomarkers—usually a protein, DNA, or RNA segment—that are specific to a host species, enabling low-level detection and source identification, even when feces from multiple species are present.

The new MST detection method uses CrAss-like phages (CLPs), a class of viruses that infect bacteria (bacteriophages), as MST markers. CLPs are the most abundant bacteriophages in the human gut, and many CLPs are only found in human intestines (and feces). While there are several known groups of CLPs, only a single group, known as Genus I, has been used as an MST marker. Therefore, the study’s researchers aimed to explore whether other group CLPs can function as MST markers and their viability compared to Genus I, as a robust MST marker would improve the ability to mitigate health risks from fecal-contaminated water.

Using polymerase chain reaction (PCR) to detect CLP DNA, the method is capable of detecting human feces-contaminated water, and is cost-effective, selective, and easy to perform.

Efficacy of the method was demonstrated in a study published in Water Research. The work was led by Ok Kyung Koo, Ph.D. and Dong Woo Kim from Chungnam National University, in collaboration with Yang Jae Kang and Dong U Woo from Gyeongsang National University.

The researchers collected fecal samples from humans and other animal species, which were subjected to DNA extraction and sequencing to detect and classify CLP viral genes. A total of 13 distinct CLP groups were identified in human gut viruses. Using these CLPs as a template, the scientists then developed specific markers for their detection via PCR and tested them for their capacity to detect human fecal contamination.

CLPs were found in 91.52 percent of human feces samples and were absent in all animal samples, except racoons. Of the 13 CLP groups classified identified, Genus VI was present in 64.4 percent of samples, nearly double that of genus I (37.28 percent). Furthermore, all 13 CLP groups showed some similarity in their gene sequences, called the major head protein gene, implying that a single marker could be used to detect multiple groups of contaminants.

The researchers believe that using PCR to detect MHP genes of Genus VI or Genus I CLPs can help improve hygiene regulations and lower public health costs through the strategic screening of sewage, wastewater, and environmental samples.