Scientists Warn: Household Drinking Water Is Spreading Dangerous Bacteria

Research identifies effective strategies for safeguarding community health.

Every year, over half a million children under the age of five die from gastrointestinal infections caused by bacteria. Most of these deaths occur in areas where access to clean drinking water, proper sanitation, and hygiene is limited. To tackle this urgent health crisis, researchers are working to understand exactly how these harmful bacteria spread.

A new study from UC Berkeley has revealed a surprising finding: the household environment, especially stored drinking water, may be a major contributor to the spread of bacteria like E. coli. Using an innovative method to track bacterial strains, the research team found that water stored in containers such as jerry cans and buckets can act as a key pathway for infection within and between homes in low-resource communities.

Published in Nature Microbiology, the study provides important new insights into how contaminated water can fuel the spread of both gastrointestinal illness and antibiotic-resistant bacteria. These findings could help shape smarter strategies to protect children’s health and stop deadly bacteria at the source.

From Animals to Water: A Shift in Focus

According to Amy Pickering, associate professor of civil and environmental engineering and the study’s principal investigator, previous studies had focused on the bacteria exchange between animals and humans. Her team decided to explore the role of drinking water and soil as under-studied pathways.

“We were interested in understanding the role of the household environment in bacterial transmission to humans,” she said. “And our findings showed that water is actually one of the most important transmission pathways for pathogenic and drug-resistant bacteria.”

To see how each of the three main pathways — human, animal, and environment — contribute to bacterial spread in these communities, Pickering’s team developed a scalable, high-throughput bacterial strain-tracking method called PIC-seq (Pooled Isolated Colonies-seq). Using this tool, researchers could sequence up to five bacterial strains per sample, instead of the conventional one strain per sample.

“PIC-seq proved to be a game changer,” said Pickering. “It enabled us to get more comprehensive views of within and between household strain sharing.”

Field Study in Nairobi

They then studied E. coli strain-sharing patterns within two households located in informal urban settlements in Nairobi, Kenya. These communal settings typically consist of compounds with a shared courtyard. As low-resource communities, they also have limited access to basic services and infrastructure, and household drinking water is often stored in jerry cans and plastic buckets.

The researchers collected human stool, poultry and dog feces, stored water, and soil samples from each household. They then cultured E. coli colonies from the samples and used PIC-seq to analyze the different strains.

Surprising Results

“We found a higher level of strain-sharing between humans and stored drinking water than between humans and domesticated animals within households,” said Daniel Daehyun Kim, a postdoctoral researcher and lead author of the study. “These findings underscore that the environment can play just as significant a role in bacterial transmission as animals — or even more so.”

While analyzing the contaminated drinking water, the researchers also identified E. coli strains carrying high-risk antibiotic resistance genes. Such genes could be passed to other bacteria through horizontal gene transfer, enabling the spread of antibiotic-resistant strains within the community, another serious health threat.

In addition, the study offered clues about potential mitigation strategies. Households with access to chlorinated water showed a lower rate of E. coli contamination in stored drinking water. Based on these findings, the researchers suggest that community-level chlorinated water may offer a practical approach to preventing the spread of bacterial and drug-resistant strains between household members as well as between different households.

“Overall, our study’s findings highlight the importance of safe drinking water in mitigating the spread of pathogenic and antibiotic-resistant bacteria,” said Kim, “which is critical to safeguarding children’s health in these communities.”

Reference: “Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements” by Daehyun D. Kim, Jenna M. Swarthout, Colin J. Worby, Benard Chieng, John Mboya, Ashlee M. Earl, Sammy M. Njenga and Amy J. Pickering, 1 June 2025, Nature Microbiology.
DOI: 10.1038/s41564-025-01986-w

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