Comparison of pathogenic bacteria in water and fecal-source samples in the Kathmandu Valley, Nepal, using high-throughput DNA microarray

Fecal contamination of water occurs from agricultural lands that use animal manure, runoff from urban surfaces, and direct discharge of untreated sewage. This study investigated and compared the presence of pathogenic bacteria using a DNA microarray targeting 941 pathogenic bacterial species/groups in water and fecal-source samples in the Kathmandu Valley, Nepal. Sixteen water samples were collected from 13 shallow dug wells, a deep tube well, a spring, and a river, whereas a total of 16 composite fecal-source samples were collected from feces of chicken, dogs, ducks, pigs, ruminants, and human sewage. Nineteen pathogenic bacterial species/groups, including nine biosafety level (BSL) 2 and one BSL 3 bacteria, were detected in >70% of both the water and fecal-source samples. Among the waterborne pathogenic bacteria identified, Helicobacter pylori, Klebsiella spp., Salmonella enterica serovars, Vibrio cholerae, and Yersinia enterocolitica were detected in both water and fecal-source samples, with detection ratios of >6% and >60%, respectively, suggesting that transmissions of these pathogenic bacteria in water might be from fecal sources. These results indicate that improper disposal of feces is occurring, causing fecal pollution in environmental waters and adversely affecting human and animal health.