Every year, over 500,000 children under five lose their lives to gastrointestinal bacterial infections globally, predominantly in areas with inadequate access to safe drinking water, sanitation, and hygiene facilities. But to alleviate this public health threat, scientists need to better understand how these pathogens spread.
To see how each of the three main pathways—human, animal, and environment—contributes 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 one conventional 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.”
The team then studied E. coli strain-sharing patterns within two households in informal urban settlements in Nairobi, Kenya. These communal areas typically feature compounds with a shared courtyard. As low-resource communities, they also have limited access to basic services and infrastructure, with household drinking water commonly stored in jerry cans and plastic buckets.
The researchers collected human stool, poultry, dog feces, and stored water and soil samples from both households. They cultured E. coli colonies from these samples and used PIC-seq to analyze the distinct strains.
“We found a higher level of strain-sharing between humans and stored drinking water than between humans and domesticated animals within households,” said lead author and CEE postdoctoral researcher, Daniel Daehyun Kim. “These findings underscore that the environment can play just as significant a role in bacterial transmission as animals — or even more so.”
Check out the full research study on the UC Berkeley Engineering website.