A bacterium capable of causing severe diarrheal illness and outbreaks of food poisoning is circulating widely through rivers and wildlife in urban and peri-urban Japan, carried largely by invasive raccoons whose feces contaminate waterways that ultimately reach human food and water supplies. A new peer-reviewed study from Osaka Metropolitan University (OMU) has used genetic, animal, and environmental water sampling to trace the transmission pathway of Escherichia albertii from raccoons through river systems to human populations.
Published in Applied and Environmental Microbiology, the study represents the first large-scale integrated surveillance of E. albertii across wildlife and environmental water within a single Japanese prefecture. Researchers detected the bacterium in 77% of water samples drawn from six of eight river systems in Osaka Prefecture, and in 56% of 122 wild raccoons tested across the same region.
An Emerging Zoonotic Pathogen Still Poorly Understood
E. albertii is an emerging zoonotic foodborne pathogen closely related to E. coli. It causes diarrhea, abdominal pain, vomiting, and fever in humans, and has been linked to multiple outbreak events in Japan and, more recently, China. The bacterium is frequently misidentified as other organisms, meaning human infections are likely underreported. Some strains produce Shiga toxin 2, a primary virulence factor associated with hemorrhagic colitis and hemolytic uremic syndrome.
The raccoon (Procyon lotor) is an invasive species in Japan, introduced for the pet trade, and its populations have expanded substantially across the country. The animals are highly adaptable omnivores with strong ties to aquatic environments, making them a plausible vehicle for introducing pathogens into the water systems that supply irrigation for crops and drinking water infrastructure.
To investigate this risk, a research team led by Associate Professor Atsushi Hinenoya from OMU’s Graduate School of Veterinary Science conducted surveillance of rivers and raccoon populations in Osaka Prefecture between 2021 and 2023, then applied whole-genome sequencing to compare strains from water, wildlife, and previously documented human clinical cases.
Genetic Fingerprinting Reveals Cross-Source Connections
The genomic analysis proved revealing. All 147 bacterial strains isolated from water and raccoon samples carried virulence genes associated with human disease. Whole-genome sequencing showed substantial genetic diversity across strains but also documented clear phylogenetic overlaps between raccoon and river water isolates. In one notable case, a strain collected from river water and a strain from a raccoon captured in the same city at roughly the same time differed by fewer than 20 single-nucleotide polymorphisms, a threshold commonly used to define epidemiological linkage in E. coli research.
Several environmental water strains also clustered genetically with human clinical isolates. One environmental strain showed only 23 single-nucleotide polymorphism differences from a strain linked to a 2017 outbreak in Tochigi Prefecture that sickened 137 people, an event traced to contaminated agricultural produce including salad ingredients. Three clinical strains differed from a raccoon-derived strain by only 6 to 9 nucleotide variants.
Importantly, bacteria were detected at upstream sampling points far from residential areas, farms, or recreational facilities, suggesting wildlife rather than human activity as the primary source of contamination. Negative samples were collected almost exclusively in winter, consistent with known seasonal declines in raccoon carriage of the bacterium.
One Health Biosurveillance Approach
The findings carry direct implications for foodborne illness surveillance and waterborne disease prevention. If E. albertii strains are continuously circulating through river systems and established wildlife populations, humans may encounter them repeatedly through contaminated irrigation water or produce. That ecological persistence also makes outbreak tracing considerably more difficult.
The researchers advocate for a One Health approach that integrates monitoring across human health, animal populations, agricultural systems, and environmental water. The team plans to investigate contamination routes more precisely, tracing pathways from raccoons and river water through agricultural products to the point of human exposure.
“The approach used in this study can be applied to other zoonotic diseases,” said Professor Hinenoya. “We hope to expand this research toward the development of comprehensive strategies for infectious disease control.”
Sources and further reading:
Tracking infectious bacteria from raccoons via rivers to humans with DNA – Osaka Metropolitan University
Integrated study on the occurrence and genomic features of Escherichia albertii in environmental water and raccoons in Japan. Applied and Environmental Microbiology