E. coli cross-contamination affects pigs and pork

By Andrew Heck

In 2018, pork contaminated with E. coli O157:H7 was served at a restaurant in Edmonton, causing more than 42 human cases of illness, including one death.

Foodborne illness has long been the bane of the agri-food industry. A first-hand encounter with the gut-churning, mind-altering discomfort and fatigue of sickness caused by contaminated food is something no-one wants to experience. While a brutal time sitting on the toilet, laid out on the couch or delirious in bed is bad enough, it can, in fact, be much worse.

Such was the case for one poor woman in March 2018, who died after eating at a restaurant in southeast Edmonton. The culprit: Escherichia coli (E. coli) O157:H7, which was consumed in a pork-based dish that was improperly cooked prior to serving. Even when bacteria like E. coli and other related pathogens are present, they can be eliminated when food is cooked thoroughly to a safe internal temperature. This is sometimes difficult when food is consumed raw, like in salad, but the problem is largely avoidable in meat, if proper handling and cooking practices are used.

In response to the 2018 outbreak, the Canadian Food Inspection Agency (CFIA) issued a recall of all products from the affected on-farm processor that supplied the restaurant and sold products to other consumers. While the recall was a necessary precaution, it resulted in some negative attention toward the farm – a regrettable reputational hit for the entire pork industry. But, as such, it became imperative for research to address the many questions being asked.

Now, a team of scientists in Alberta is coming out with answers. At the 2021 Banff Pork Seminar, postdoctoral researcher Peipei Zhang, with Xianqin Yang’s research group at Agriculture and Agri-Food Canada’s (AAFC) Lacombe Research and Development Centre, presented a poster exploring one aspect of the issue, prompting a closer look at the bigger picture.

Killer E. coli in pork?

E. coli O157:H7 is known to exist in cattle, often being transmitted at feedlots. But for a long time, no-one suspected pigs too could be affected.

Until the 2018 incident, pork had never been implicated in any deaths in Canada due to E. coli. This realization caused confusion among industry observers, even to the point that some initially doubted it was possible.

“When I first heard that someone had died from eating pork contaminated with E. coli O157:H7, I didn’t believe it,” said Saida Essendoubi, a surveillance scientist with Alberta Agriculture and Forestry, and the leader of the E. coli research group. “How can this be? We had only seen this in beef before, but it turns out pigs are vulnerable too, even at the farm where this pork came from, which has very good biosecurity.”

What makes E. coli O157:H7 potentially lethal? ‘Shiga toxins,’ named after Kiyoshi Shiga, a Japanese researcher who discovered Shigella dysenteriae, in 1897. Eight decades later, in 1977, researchers in Ottawa with the Bureau of Microbial Hazards, Health Protection Branch, Health and Welfare Canada discovered the Shiga toxin normally produced by Shigella dysenteriae in a line of E. coli, which includes the O157:H7 strain.Ingestion of Shiga toxins can result in abdominal pain and watery diarrhea. In serious instances, these symptoms can be life-threatening, as was the 2018 case in Edmonton.

Cattle are a natural reservoir of E. coli O157:H7. In contrast, studies have found very low prevalence of the organism in pigs and, consequently, very few pork-related E. coli O157:H7 outbreaks have ever occurred. However, in addition to the 2018 case, two more previous non-lethal outbreaks were discovered in Alberta in 2014 and 2016, attributed to the consumption of contaminated pork at the food service level.

Finding the source of E. coli O157:H7 in Alberta meat

With the consideration that E. coli O157:H7 is known to inhabit cattle feedlots in southern Alberta, an obvious red flag was raised regarding premises that keep both cattle and pigs on-site, with assembly yards and mixed farms being places of interest.

“When people move from one part of a site to another without changing their boots, for example, there is potential for pathogen transmission,” said Javier Bahamon, Quality Assurance and Production Manager, Alberta Pork. “Back when porcine epidemic diarrhea (PED) first spread in Alberta, the question was whether the four cases were directly connected. Three of the four impacted sites were within a 20-kilometre radius of each other, suggesting farm-to-farm spread. But while no individuals or vehicles were found to have travelled directly between those farms, there is a possibility that individuals or vehicles from those farms crossed paths with each other at a neutral site. The possibility for this kind of transmission is alarming not only for spreading PED but also E. coli O157:H7, considering how many cattle premises are in proximity to hog premises in Alberta.”

To evaluate the southern Alberta assembly yards and mixed farms’ connection to the meat processing sector, Essendoubi, Bahamon, Yang and other researchers began collecting carcass and colon samples at provincially inspected abattoirs across the province.

More than 500 carcass samples were also analyzed for generic E. coli and aerobic colony count, which refers to the total number of bacteria able to grow in an oxygenated environment – an indicator of microbial quality of food. Of all the carcass samples collected, nine were confirmed positive for E. coli O157:H7, representing nearly two per cent of the total, which is consistent with existing literature worldwide. Similarly, seven of the colon samples tested positive. These positives were found across five of 39 abattoirs visited, from hogs originating at eight different farms.

Understanding the E. coli O157:H7 genome

Matrix of test results categorized by various isolates, animal species (pigs or cattle) and location (farm or plant).

To explore the potential source of E. coli O157:H7 contaminating pork, Zhang undertook an investigation into the phylogenetic relatedness of the bacteria in pigs and cattle on-farm, along with pork processing facilities. This work was led by Yang in collaboration with other researchers, with funding from Alberta Innovates.

Whole genome sequencing is a promising technology for tracing the origin of bacteria. This technique was the first choice for discovering the relationships between E. coli O157:H7 in pigs and cattle on-farm and within packing plants. Because E. coli O157:H7 genome sequences originating from pigs are limited in public databases, Yang and Essendoubi, in collaboration with Kim Stanford and Tim Reuter from the University of Lethbridge, decided to sequence E. coli O157:H7 strains gathered from pig and cattle feces, for comparison.

The study relied on whole genomes obtained first-hand by the researchers, in addition to data sourced from the U.S. National Center for Biotechnology Information – known as ‘GenBank’ – which was the best source of existing data at the time. Gene subtyping based on whole genome sequencing data revealed that nearly 95 per cent of the samples were closely related strains, with further analysis indicating that these strains all had a common and recent ancestor.  

The researchers decided to dig deeper into the genetic characteristics of E. coli O157:H7. Nearly 61 per cent of pig isolates harboured one Shiga toxin variant, while 70 per cent of the cattle isolates carried two variants. The variant harboured by most of the pig isolates is associated with more severe outcomes. Analysis also shows that similar strains can be repeatedly isolated from pig gut contents over a period of up to two years, strongly suggesting pigs can, in fact, be a source of E. coli O157:H7 – the definitive finding that confirmed suspicions.

Never before could it be proven that sites common to cattle and pigs were able to support the transmission of E. coli O157:H7, uncloaking the mystery of the contaminated, undercooked restaurant pork and setting the research team on the path to supporting an enhanced approach to managing the disease risk.

Preparing the industry for the future

Biosecurity protocols, including rodent control, will be crucial for producers to stem the spread of E. coli O157:H7.

Regardless of the reasons surrounding the 2018 death connected to E. coli O157:H7, the entire Canadian pork industry is doing its part to prevent any further harm by better understanding the issue and preparing stakeholders to manage risks.

“Adapting and performing biosecurity assessments to account for E. coli O157:H7 will be an important next step,” said Essendoubi. “Alberta Agriculture and Forestry, working with Alberta Pork and other organizations, will begin to focus its attention on helping industry partners manage risks.”

Observable clinical signs of illness related to E. coli O157:H7 are non-existent, meaning efforts to educate producers will have to be very proactive. From clothing and visitor biosecurity protocols to better rodent management in barns, vulnerabilities within production remain an ongoing threat.

“We have to get producers to take this seriously,” said Bahamon. “Foodborne illness is a human health matter. Consumers care. As much as producers are rightly concerned with swine diseases and their impact on production, our social licence to operate as an industry depends on public trust in our food safety systems.”

When and where will the next E. coli O157:H7 outbreak connected to pigs occur? Hopefully, never and nowhere, but even with due attention to the matter, the industry may have to expect that future outbreaks are, unfortunately, not out of the question. Producers can and should protect themselves by reviewing their on-farm biosecurity.

Organizations like Alberta Pork, Alberta Agriculture and Forestry, Alberta Innovates, AAFC, CFIA and other industry partners are currently working to ensure all stakeholders have the knowledge and tools they need to reinforce food safety and consumer confidence.