A loop-mediated isothermal amplification assay for the rapid and quantitative tracking of fecal contamination sources in water.

Fecal contamination in water poses a serious threat to public health and the ecological environment. Numerous qPCR-based methods have been used to identify the source of fecal contamination, but this method relies on expensive equipment, well-established laboratory conditions, and experienced personnel, significantly reducing the timeliness of identifying contamination sources. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for tracking the sources of fecal contamination to rapid identifying and quantifying humans, ruminants, pigs, and poultry fecal contamination. The results demonstrated that LAMP assay enabled us to easily and quickly (<30 min) detect associated gene of the host gut microbes for tracking of fecal contamination sources, exhibiting a same detection level of 100 gene copies/μL as lab-based qPCR. Compared to LAMP molecular markers of other bacterial genera and bacteriophages, the LAMP molecular markers of Bacteroidales showed a higher sensitivity and detection concentration. The majority of the non-target species (96.9%) showed little effect on the LAMP marker genes of the target species. Moreover, the LAMP assay was used to identify a multiple fecal contamination and spatial distribution characteristics in the Liuxi River basin. The detection frequency and abundance of human-associated marker genes were the highest, followed by pig-associated marker gene; the mean concentration of human- and pig-associated marker gene in tributaries were higher than that in the mainstem. This LAMP assay could be used to easily and quickly identify the sources of fecal contamination and contribute in the control and treatment of fecal contamination in water.