Researchers mapping genome of harmful E. coli

Article By Emmanuel Bumunang, Tim McAllister Published January 5, 2023
Article Source: Researchers mapping genome of harmful E. coli - Canadian Cattlemen

News Roundup from the January 2023 issue of Canadian Cattlemen

Alberta researchers at Agriculture and Agri-Food Canada and the Universities of Alberta, Calgary and Lethbridge are deciphering the genetic code of E. coli bacteria to map which strains may trigger disease in humans or be carried for a long time by apparently healthy people. 

E. coli is part of the normal flora in the digestive tract of humans and animals. Normally, it competes with other microbes for nutrients and space, which helps eliminate harmful bacteria and maintain the normal balance of the entire microbial population in the digestive tract. Some E. coli strains also help produce vitamins. However, for unknown reasons, some strains have acquired virulence genes that can produce toxins that are harmful to humans. One of these harmful strains is E. coli O157:H7, which can produce Shiga toxins that cause severe food poisoning with bloody diarrhea and vomiting, and in severe cases kidney failure. 

Shiga toxin-producing E. coli O157:H7 is harboured by healthy cattle that shed it in their feces. Shedding may vary between cows in a herd and those that shed more bacteria or over a long time are called super shedders. E. coli can come into contact with meat during food processing, or with vegetables or fruits through contaminated water or soil, with these sources being increasingly linked to E. coli outbreaks. However, there is also growing evidence that humans can be carriers without developing clinical symptoms and may also contaminate food through poor hygienic practices. 

Shiga toxin-producing E. coli O157:H7 is highly infectious. As few as 10 cells can cause disease, with the young, old, immunocompromised and pregnant women being considered high-risk groups. 

Supportive therapy with hydration to maintain electrolyte balance is the most reliable treatment in humans. Antibiotics are not often administered due to concerns that such a practice may increase toxin production. However, there is some interest in using antibiotics to potentially treat people who are long-term, asymptomatic carriers of Shiga toxin-producing E. coli. Based on these findings, not all E. coli isolates are created equal. Therefore, it would be beneficial to have a method that could differentiate those isolates in cattle that may cause disease in humans from those that do not. Likewise, it would be useful to identify strains that cause disease in humans as well as those that can persist in apparently healthy individuals. 

Identifying the genetic makeup of these E. coli isolates using a process known as whole genome sequencing may help accomplish these objectives. 

Whole genome sequencing can discriminate between highly infectious E. coli strains that can cause disease and those that do not. It may also be able to identify strains that are common in cattle from those that are more likely to reside and cause disease in humans. Whole genome sequencing can also be an important tool in food safety, as it can identify closely related E. coli from outbreak events. Its high level of sensitivity can differentiate strains from similar geographic regions or different origins. 

Researchers analyzed Shiga toxin-producing E. coli O157:H7 from cattle and human clinical cases in the same region of Alberta. The samples were collected from 2007 to 2015. The findings revealed that the genes coding for Shiga toxins were in different positions in the human and cattle E. coli genomes. It is possible that adapted strains may be cycling between humans and cattle, or that humans may be a more important reservoir for disease-causing strains than previously thought. If the trait that differentiates the strains that infect cattle and humans is stable, then it could be used to screen and monitor E. coli O157:H7 in the future

Researchers are digging deeper by exploring whole-genome long-read sequencing to confirm more of the genetic differences between cattle and human strains. They are also looking at whether mobile genetic elements are transferring toxin genes with the genome of Shiga toxin-producing E. coli O157:H7, or between strains. 

This project was a joint effort by researchers at Agriculture and Agri-Food Canada (Drs. Tim McAllister and Rahat Zaheer), Canadian Food Inspection Agency (Dr. Chad Laing) and the Universities of Alberta (Drs. Linda Chui and Leluo Guan), Calgary (Drs. Dongyan Niu and Emmanuel Bumunang) and Lethbridge (Kim Stanford).