Genetic microbial faecal source tracking: rising technology to support future water quality testing and safety management

Abstract

Recent developments in water resource monitoring have increased the demand for the reliable identification of faecal pollution sources, also defined as microbial (faecal) source tracking (MST). Standardized faecal indicator bacteria (SFIB) enumeration does not directly support MST, as SFIB occur in animal and human sources. The aim of this study was to rigorously evaluate the applicability of host-associated faecal genetic MST markers detected by quantitative PCR (qPCR) at representative Austrian water resources (ground-, surface-, raw and treated wastewater, n = 196 samples) with high importance for the water management sector. Groundwater covered a gradient of non- (i.e., deep wells) to surface influenced resources (i.e., karst and shallow wells). In addition, single faecal excreta from humans as well as representative livestock and wildlife species were collected to evaluate the faecal source-specificity and -sensitivity of the MST assays. Genetic MST marker resistance against UV irradiation was evaluated in on-site ground and wastewater treatment installations. Bacteroides-based human- (HF183II, BacHum), ruminant- (BacR), and pig-associated (Pig2Bac) MST marker qPCR quantification was performed in concert with cultivation of E. coli, intestinal enterococci, and Clostridium perfringens (SFIB diagnostics). The selected MST makers revealed high faecal source identification capacity for the Austrian water compartments and quantitatively reflected the selected faecal pollution gradient. The study also demonstrated that SFIB data can efficiently be combined with MST data to solve previously unanswered questions in water safety monitoring and management (e.g., support pollution source-targeted catchment protection, hazard assessment, and health risk management). Further research and development needs are discussed to exploit the full power of MST technology. In conclusion, this study illustrates the capacity of molecular faecal pollution diagnostics to revolutionize water quality testing in the decades to come.

Using Watershed Characteristics for Improving Fecal Source Identification

“…The present study is consistent with these findings; both watersheds displayed a high prevalence of ruminant pollution, most likely related to high livestock densities and widespread use of tile drainage. In addition to basic land use classification, a variety of other studies in both tropical and temperate environments worldwide, have made associations between microbial indicators, hydrology, water chemistry, and land use characteristics to identify sources of fecal pollution in a variety of water sources, streams, groundwater, and river systems, (Frick et al, 2020; Jent et al, 2013; Lyons et al, 2021; Sekar et al, 2021; Steinbacher et al, 2021; Wiesner-Friedman et al, 2022). These studies highlight the importance of connecting pathogen contamination with other land use and chemical characteristics to confirm the identification of non-point sources of fecal contamination.…”

Microbial source tracking of fecal contamination in stormwater runoff

“…MST is a group of polymerase chain reaction (PCR)-based methods that identify an individual type of fecal contamination in water, traditionally quantified through concentrations of FIB in the sample (Wuertz et al 2011;Steinbacher et al 2021). Quantitative PCR (qPCR) is an especially useful type of MST, as the results can be rapidly produced (Ahmed et al 2018).…”