Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?

Katalin Demeter, Rita Linke, Elisenda Ballesté, Georg Reischer, René E Mayer, Julia Vierheilig, Claudia Kolm, Margaret E Stevenson, Julia Derx, Alexander K T Kirschner, Regina Sommer, Orin C Shanks, Anicet R Blanch, Joan Rose, Warish Ahmed, Andreas H Farnleitner

Research output: Journal article (peer-reviewed)Journal article

5 Citations (Scopus)


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.

Original languageEnglish
Article numberfuad028
JournalFEMS Microbiology Reviews
Issue number4
Early online date07 Jun 2023
Publication statusPublished - 01 Jul 2023


  • DNA/RNA analysis
  • faecal and MST markers
  • faecal indicator
  • faecal pollution microbiology
  • microbial source tracking
  • systematic review

ASJC Scopus subject areas

  • General Medicine


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