TY - JOUR
T1 - Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?
AU - Demeter, Katalin
AU - Linke, Rita
AU - Ballesté, Elisenda
AU - Reischer, Georg
AU - Mayer, René E
AU - Vierheilig, Julia
AU - Kolm, Claudia
AU - Stevenson, Margaret E
AU - Derx, Julia
AU - Kirschner, Alexander K T
AU - Sommer, Regina
AU - Shanks, Orin C
AU - Blanch, Anicet R
AU - Rose, Joan
AU - Ahmed, Warish
AU - Farnleitner, Andreas H
N1 - Funding Information:
This work was supported by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (GFF) (grant number LSC 19-016 ‘Future Danube’), by the Vienna Science and Technology Fund (WWTF) (grant number ESR17-070), and by the research project ‘Vienna Water Resource Systems 2020+’ (ViWa2020+), in cooperation with the City of Vienna (Vienna Water, MA31). The content does not necessarily represent the views of the Province of Lower Austria or the Gesellschaft für Forschungsförderung Niederösterreich as the funding agency. Neither the province of Lower Austria nor the funding agency can, therefore, be held responsible for the content.
Funding Information:
The authors acknowledge TU Wien Bibliothek for financial support through its Open Access Funding Programme. The authors are thankful to Andreas Pacher from TU Wien Bibliothek for help with database searches and for critical discussion on paper evaluation metrics. We thank also Dr. Mats Leifels for providing useful discussion and references. Information has been subjected to U.S. EPA peer and administrative review and has been approved for external publication. Any opinions expressed in this paper are those of the authors and do not necessarily reflect the official positions and policies of the U.S. EPA. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use. This is a joint research effort of the Interuniversity Cooperation Centre for Water & Health ( www.waterandhealth.at ) and the Global Water Pathogen Program (GWPP) initiative ( www.waterpathogens.org ).
Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of FEMS.
PY - 2023/7/1
Y1 - 2023/7/1
N2 - 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.
AB - 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.
KW - DNA/RNA analysis
KW - faecal and MST markers
KW - faecal indicator
KW - faecal pollution microbiology
KW - microbial source tracking
KW - systematic review
UR - http://www.scopus.com/inward/record.url?scp=85165782853&partnerID=8YFLogxK
U2 - 10.1093/femsre/fuad028
DO - 10.1093/femsre/fuad028
M3 - Journal article
C2 - 37286726
SN - 0168-6445
VL - 47
JO - FEMS Microbiology Reviews
JF - FEMS Microbiology Reviews
IS - 4
M1 - fuad028
ER -