New research suggests that nearly 1 in 5 urinary tract infections (UTIs) in Southern California may be caused by strains of Escherichia coli that originated in food-producing animals.
For the study, a team led by scientists at George Washington University and Kaiser Permanente Southern California (KPSC) conducted molecular analysis of more than 5,700 extraintestinal pathogenic E coli (ExPEC) isolates collected from UTI patients and retail meat samples from stores in the neighborhoods where those patients lived. Using comparative genomic analysis and a model they developed to infer the host origin of each isolate, they found that 18% of the UTIs were linked to ExPEC strains that came from the meat.
They also discovered that UTIs in patients from high-poverty neighborhoods were 60% more likely to be caused by these zoonotic (animal-to-human) ExPEC strains.
The findings were published yesterday in the journal mBio.
“These findings underscore the contribution of zoonotic ExPEC to the UTI burden in Southern California and the need for targeted interventions to reduce risk in vulnerable communities,” the study authors wrote.
An underappreciated cause of UTIs
The findings build on research that Lance Price, PhD, founding director of George Washington University’s Antibiotic Resistance Action Center, and his colleagues have been conducting for more than a decade.
In a study published in 2018, they found that a strain of E coli that has caused serious UTIs around the world was prevalent in chicken and turkey meat. Then, in a follow-up study in 2023 that used similar methods to the current study, they found that 8% of E coli isolates from human UTIs in Flagstaff, Arizona, were linked to retail meat sold in local stores and likely originated from food-producing animals.
“It was surprising that it was more than twice as high,” Price told CIDRAP News, referring to the new results. “And that led us to try to figure out why.”
Foodborne E coli is generally associated with gastrointestinal illness and certain diarrhea-causing strains, such as Shiga toxin–producing E coli, are tracked by industry and US health officials to make sure they are not contaminating the food supply and posing a risk to people. But the research Price and his colleagues have been conducting suggests that foodborne ExPEC strains that enter the urinary tract are an underappreciated cause of the 8 million UTIs diagnosed each year in the United States.
The kind that kills the most people are the extraintestinal pathogenic E coli, the kind that live in the gut with no symptoms.
Although most UTIs are mild, they can progress to more serious invasive infections and sepsis if the infection gets into the bloodstream.
“When most people hear E coli, they think about diarrhea and these dramatic foodborne outbreaks,” he said. “But the kind that kills the most people are the extraintestinal pathogenic E coli, the kind that live in the gut with no symptoms. If it gets in the urinary tract, it has these special features that allow it to cause disease.”
18% of E coli came from food animals
To determine the percentage of UTIs in Southern California that could be attributed to zoonotic ExPEC strains, the research team—which also included scientists from the University of Cambridge, University of Oxford, Johns Hopkins University, and Statens Serum Institut—performed whole-genome sequencing on 2,349 human clinical E coli isolates collected from KPSC regional labs from February 2017 through May 2021. The patients were predominantly Hispanic (37.0%) and non-Hispanic White (31.7%) and resided in areas with low (42.2%) and medium family poverty rates (44.5%).
The investigators also sequenced 3,379 E coli isolates collected from retail samples of chicken, turkey, beef, and pork that were bought weekly from major grocery chains in the region. E coli contamination was highest in turkey samples (82%), followed by chicken (58%), pork (54%), and beef (47%), and was higher in meat samples from stores in high poverty areas.
In addition to comparing the core genomes of the human and foodborne E coli isolates, the researchers were looking for the presence of 17 human- and animal-associated mobile genetic elements (MGEs). Their statistical model combines this information to help determine the origin of the isolate. If animal-associated MGEs are prevalent in E coli collected from UTI samples, that’s an indication the source was an animal.
“When we see E coli in people that are carrying these chicken-adaptive mobile genetic elements, we can not only say that it came from chicken, but it probably came from chicken recently,” Price explained.
The model estimated that 17.7% of the human clinical E coli isolates originated from food-producing animals, primarily chickens and turkeys. The researchers also found that a subset of E coli lineages, primarily those from poultry products, appeared to have “enhanced capacity” to cause zoonotic UTIs. Urine samples from women were significantly more likely to have zoonotic ExPEC strains than samples from men (19.7% vs 8.5%).
Zoonotic strains less resistant to antibiotics
Notably, the zoonotic ExPEC strains were less likely than the non-zoonotic strains to be resistant to the antibiotics commonly used to treat UTIs.
This finding, the authors say, may support the effectiveness of efforts by the Food and Drug Administration (FDA) to limit use of medically important antibiotics in livestock. Although the FDA has been criticized for not doing more, the authors note that, in countries where there is little regulation of antibiotic use in livestock, studies have found significantly higher levels of resistance to medically important antibiotics in bacteria spread from animals to people.
Rigorous antibiotic stewardship is needed in human and animal medicine.
Gail Hansen, DVM, a public health and veterinary consultant who was not involved in the study, said the link between human UTIs and E coli from chickens and other food-producing animals is another reminder of why antibiotic stewardship is important.
“Rigorous antibiotic stewardship is needed in human and animal medicine,” Hansen said in an email. “We can’t squander the precious resource of antibiotics anywhere.”
Link between poverty rate, zoonotic E coli
But what was even more surprising was that highest proportion of zoonotic ExPEC isolates (21.5%) was identified in patients from high-poverty areas. “After adjusting for age, sex, and race/ethnicity, individuals residing in a high-poverty area had a 1.6-fold increased risk of zoonotic ExPEC infections compared to those in low-poverty areas,” the authors wrote.
Although the factors underlying the correlate between the poverty rate and foodborne UTIs isn’t entirely clear and needs further study, Price says he has some ideas. He notes that when he first began this line of research, he noticed that the chicken he bought from stores in poorer neighborhoods in Washington, DC, tended to be poorly packaged and “bloated with saline” that was likely contaminated with bacteria and could leak onto other groceries.
Although they didn’t compare retail meat packaging in stores from different neighborhoods in this study, Price says he would like to see if that could be a factor.
“I do think that you could have the poorest-quality products in the poorest packaging being marketed in the poorest neighborhoods,” he said. “It’s a question worth investigating.”
For now, though, Price says recognizing meat as a potential source of exposure to zoonotic E coli could help reduce the burden of UTIs. One place to start would be for industry or regulatory agencies to start testing meat for other types of E coli, and not just the toxigenic strains that cause gastrointestinal illness.
“Almost every piece of chicken or ground turkey I test has E coli in it,” he said. “We should be doing more to decrease contamination.”
When you open that package, just assume you’ve splattered some bacteria in your kitchen.
Until that happens, he added, consumers should follow safe food-handling procedures, including thorough cooking of meat, washing hands and surfaces, and avoiding cross-contamination.
“When you open that package, just assume you’ve splattered some bacteria in your kitchen; assume every piece of meat is contaminated, and handle it that way,” he said.
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