Genetic markers to trace the origin of fecal contamination in water: a systematic review and meta-analysis

Fecal contamination of water bodies remains one of the main challenges for the protection of public health and aquatic ecosystems, especially in watersheds subjected to intense anthropogenic pressure. Although traditional microbiological indicators, such as thermotolerant coliforms and Escherichia coli, are widely used to assess water quality, they do not allow the identification of the source of contamination, limiting the effectiveness of environmental mitigation and management strategies. In this context, host-specific genetic marker-based methods employed in tracing the origin of fecal contamination (MST) emerge as important tools for discriminating between human and animal sources, including cattle, pigs, poultry, and other reservoirs. These genetic targets consist of bacterial, viral, or mitochondrial markers, which are widely used to differentiate sources of fecal contamination in aquatic environments. In view of the increasing diversity of proposed molecular markers, the methodological variations employed and the differences observed in analytical performance and environmental applicability, this study aims to map, systematize and critically analyze the main genetic markers of human and animal fecal contamination used in aquatic systems, with emphasis on their genetic targets, detection methods, environmental contexts of application and limitations, delimiting the current state of knowledge and identifying gaps for future research.