New method detects contamination of human feces in water

The presence of human waste in sewage overflows or stormwater runoff that eventually finds its way into rivers and lakes is a significant risk to public health. As a result, it is imperative that water bodies and samples are continuously tested for the presence of human faecal contamination. Conventionally, testing for faecal contamination involves detection of faecal indicator bacteria (FIB), such as E. coliby adding a drop of the sample water to a microbial culture medium. While FIB detection is cheap and simple, the method cannot be used to detect low-level contamination. This method is also unable to determine the source of the infection.

Microbial source monitoring (MST) has the potential to overcome these challenges by detecting biomarkers—typically a segment of protein, DNA, or RNA—that are specific to a host species. This allows MST to detect low-level contamination in sewage, drinking water, lakes, etc., and to identify hosts, even when feces from multiple species are involved.

CrAss-like phages (CLPs), a class of bacteria-infecting viruses (bacteriophages), are hailed as a promising group of MST markers. CLPs are the most abundant bacteriophages in the human gut, and many CLPs are found only in human intestines (and feces). While there are many known CLP groups, only one group, known as genus I, has been used as an MST marker. This raises questions about whether the other CLP groups also function as MST markers and their viability compared to genus I.

Now, in a new study, Dr. detection of water contaminated with human faeces. The method uses polymerase chain reaction (PCR) to detect CLP DNA, making the method cost-effective, selective and easy to perform. The study was published in volume 266 of Water research on November 15, 2024 and available online on August 24, 2024.

“The primary objective of this study was to improve the efficiency and accuracy of detection methods used to assess specific faecal contamination.” said Dong Woo Kim. Adding further, he says, “A robust MST indicator would greatly aid our ability to mitigate health risks from faecal-contaminated water.”

To test the effectiveness of this method, the researchers collected stool samples from selected human volunteers. Fecal samples from wild animals such as dogs, deer, cats, birds and raccoons were also included in the experiment to test the specificity of the detection method. DNA extraction and sequencing was then performed to detect and classify the CLP virus genes. 13 different CLP groups have been identified in human enteroviruses. Using these CLPs as a template, the scientists then developed specific markers to detect them by PCR and tested them for their ability to detect contamination from human feces.

The results of this study were encouraging. CLPs were found in 91.52% of human faecal samples and were absent in all animal samples except raccoons. Of the 13 classified CLP groups identified, genus VI was present in 64.4% of the samples, almost twice that of genus I (37.28%). In addition, all 13 CLP groups showed some similarity in their gene sequences, called the major head protein gene. This implied that a single marker could be used to detect multiple groups of contaminants.

“Our method shows that the VI gene is a strong marker of MST in the Korean population. The use of PCR to detect MHP genes of genus VI CLPs, or even genus I, may be a practical approach to monitor water contamination from human feces. I expect that our method can, over time, improve sanitation regulations and reduce public health costs through the strategic control of sewage, effluent and various environmental samples.” Dr. Ok Kyung Koo concludes.

In summary, the scientists concluded that CLPs, especially genus VI, could be used as viable MST markers able to specifically detect human faecal contamination. This was noteworthy as human-specific and selectively targeted MST markers can significantly influence sanitation regulations, reducing public health costs through their application in the control of liver, sewage, sewage and of various environmental samples.