Citation:

Demeter, K., R. Linke, E. Balleste, G. Reischer, R. Mayer, J. Vierheilig, C. Kolm, M. Stevenson, J. Derx, A. Kirschner, R. Sommer, O. Shanks, A. Blanch, J. Rose, W. Ahmed, AND A. Farnleitner. Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet? FEMS Microbiology Reviews. Oxford University Press, OXFORD, Uk, 47(4):fuad028, (2023). https://doi.org/10.1093/femsre/fuad028

Impact/Purpose:

Despite considerable progress, more than 800,000 people still die each year across the world from diarrheal disease, resulting from unsafe drinking water, sanitation, and hygiene. While there is clear evidence that current management approaches reduce the health risk related to water exposure and consumption, there is a constant, urgent need for more comprehensive microbiological assessment approaches. For well over 100 years, fecal pollution assessment of water has relied on the culture-based methodologies. Over the past 20 years, genetic-based methods using PCR, qPCR, dPCR, and high throughput sequencing have been developed. This manuscript reviews more than 1,000 scientific articles and provides a critical discussion of key method application areas for genetic fecal pollution diagnostics. Findings should be of interest to any stakeholder interested in the use of genetic methods for fecal pollution related water quality management.

Description:

The impacts of nucleic acid-based methods - such as PCR and sequencing - to detect and analyze indicators, genetic markers or molecular signatures of microbial faecal pollution in health-related water quality research were assessed by rigorous literature analysis. A wide range of application areas and study designs has been identified since the first application more than 30 years ago (>1100 publications). Given the consistency of methods and assessment types, we suggest defining this emerging part of science as a new discipline: genetic faecal pollution diagnostics (GFPD) in health-related microbial water quality analysis. Undoubtedly, GFPD has already revolutionized faecal pollution detection (i.e., traditional or alternative general faecal indicator/marker analysis) and microbial source tracking (i.e., host-associated faecal indicator/marker analysis), the current core applications. GFPD is also expanding to many other research areas, including infection and health risk assessment, evaluation of microbial water treatment, and support of wastewater surveillance. In addition, storage of DNA extracts allows for biobanking, which opens up new perspectives. The tools of GFPD can be combined with cultivation-based standardized faecal indicator enumeration, pathogen detection, and various environmental data types, in an integrated data analysis approach. This comprehensive meta-analysis provides the scientific status quo of this field, including trend analyses and literature statistics, outlining identified application areas, and discusses the benefits and challenges of nucleic acid-based analysis in GFPD.

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