If you've had a urinary tract infection, you're in good company. About 60% of women will develop one in their lifetime. UTIs lead to more than a million emergency room visits each year and more than $2 billion in medical costs.

Many of these infections are caused by common strains of E. coli bacteria that humans have lived with for millennia. But now researchers are investigating an unsettling source of some of the illness: the meat supply.

UTIs make urinating painful or difficult and can interfere with sex, sleep and exercise. Sometimes they can cause fever or chills. But since they can be treated with antibiotics, they've been considered more of a nuisance than a public health problem. Recently though, multi-drug resistance to some of the bacteria, including strains of E. coli, that cause UTIs has become an increasing worry.

But many of the more than 700 known strains of Escherichia coli are harmless. So the authors of a new study set out to solve a mystery: Which strains cause infections, and where do they come from?

They had a hunch that the U.S. animal agriculture system could be a likely culprit.

Both farm animals and humans have some strains of E. coli bacteria in their guts. When farm animals are slaughtered, the bacteria from their guts can contaminate raw meat, which can in turn contaminate kitchen surfaces during cooking.

A team of researchers spent one year collecting samples of raw meat in Flagstaff, Ariz., to find out if there's an overlap between the strains of E. coli in the meat supply and the strains that can make people sick.

"We sampled all the chicken, turkey and pork from every grocery store in the city twice per month," explains Lance Price, a professor at George Washington University Milken School of Public Health and the founding co-director of the Antibiotic Resistance Action Center.

They also collected urine samples from the Flagstaff Medical Center from people who were hospitalized with UTIs.

In their study, published in the scientific journal One Health, the researchers found that about 8% of UTIs in Flagstaff could be attributed to bacteria from meat. Nationwide, they estimate as many as 640,000 infections each year are caused by foodborne E. coli strains from animals.

"Our study provides compelling evidence that dangerous E. coli strains are making their way from food animals to people through the food supply and making people sick," Price says.

Genomic sleuthing clarifies the link with livestock

To pin down the connection, the researchers brought both the meat and urine samples back to their laboratory and cultured for E. coli, explains co-author Paul Keim, the executive director of the Pathogen and Microbiome Institute at Northern Arizona University. They performed genomic sequencing to inspect the microbes' DNA.

This helped them identify segments of DNA from the bacteria that are specific to strains from animals, and others that are specific to strains in people. "We started recognizing that, hey, here's these little packages of DNA that are really strongly associated with chicken," Price explains. Others can be strongly associated with pork, and others with people.

"The genomic analysis allowed us to match up a number of different strains," explains Keim.

The degree of overlap between the E. coli strains from meat and those found in samples from patients with UTIs was striking, says Tim Johnson, a professor at the College of Veterinary Medicine at the University of Minnesota who studies poultry diseases and genomics.

"When I first saw the data, I was pretty overwhelmed at the connectivity," Johnson says, though he says the study falls short of proving that the UTIs were caused by E.coli from meat. He points to the other ways the bacteria can contaminate the food supply. For instance, they can get into irrigation water and contaminate crops.

Big picture, Keim, says, the study shows "there's lots of E. coli strains out there that cause UTIs and you can get them through the food supply."

Stopping human disease may start on the farm

The researchers plan to continue to trace the connection between the food supply and human UTIs. The study allowed them to create a data platform to which they hope to build on. It's similar to how the FBI developed a database of criminal's DNA fingerprints that they can search to solve crimes, explains Keim. "We didn't have that for E. coli," or for UTIs until doing this study, he says.

This kind of knowledge could lead to new strategies to prevent the spread of bacteria that cause UTIs.

For instance, the study points to two E. coli strains that have particularly high virulence, including the ST131-H22 strain, which has been found in poultry operations. A previous study showed this strain may be a vehicle for human infection.

It turns out this strain is also causing disease in birds in poultry operations, so Johnson says some farmers vaccinate their flocks against it. "They use what's called an autogenous vaccine," Johnson explains. Those are customized for the flock from strains of bacteria isolated from animals in the flock. He says a better understanding of the overlap between human disease and animal disease, can help farmers take proactive prevention steps.

"If you're finding a problematic strain that's killing chickens or turkey, that could also be a food safety threat, they can make vaccines against those strains to try to eliminate them from the barns," Johnson says.

Ways to prevent UTIs

UTIs involve a complex interplay of bacteria, our microbiomes, immune systems and anatomy, says Dr. Michelle E. Van Kuiken, a urologist who specializes in female pelvic medicine, at the University of California, San Francisco. And Van Kuiken says patients need to understand they may get sick because of factors beyond their personal control.

"We're seeing this connection and we need to be cognizant about how large-scale animal agriculture could be impacting human health," Van Kuiken says. "To some extent, women have been done a disservice by them thinking it's something they're doing wrong or things that they can modify," she adds.

Though some of what's causing them may be out of your control, there are evidence-based tips worth trying to prevent recurrent UTIs.

1. Understand your anatomy

People born with female anatomy are more prone to urinary tract infections, explains Elodi Joy Dielubanza, a urologist at Brigham and Women's Hospital. The urethra, which carries urine from the bladder outside the body, is typically shorter in women and it's in very close proximity to the anus.

The way the E. coli ends up invading the urinary tract is kind of gross, but the bottom line is that the bacteria comes out in our poop. And, if you don't wipe right (from front to back), it can end up in the urethra where it can invade the urinary tract.

Sex can play a role too. During penis in vagina sex, the bacteria – which can live in the tissue near the anus – can travel along the penis toward the entrance of the urethra. That's why it's smart to urinate after sex to flush out some of the bacteria.

2. Stay hydrated

It's important to consume enough fluids to maintain adequate urine production, says Dielubanza. "Our body's best defense against invading bacteria is to flush it away," she says. "I like to advise my patients to maintain at least a daily intake of six cups of water."

3. Be careful with kitchen hygiene

E. coli can not survive high temperatures, so if you cook your meat to recommended minimum temperatures, you will kill off the bacteria.

The bigger risk may be poor kitchen hygiene, says University of Minnesota's Tim Johnson. "It's a common misperception that most of the transmission from chicken to human occurs by eating undercooked meat. And the fact is that the vast majority of people fully cook [it], especially poultry," he says.

Pay attention to utensils that have touched raw meat, like the cutting board, knife and spatula. "Even though you think you may have washed them thoroughly, maybe you didn't," Johnson warns. Raw meat liquid can also get on the counter surfaces, so pay attention to where it seeps out and clean it up.

The USDA has tips on how to prevent cross-contamination in the kitchen and when you're outdoors on the grill.

4. Supplements may help prevent recurrent infections

Several studies show that cranberry supplements can help reduce the risk of recurrent UTIs, according to a review by the American Urological Association. Compounds in cranberries, known as proanthocyanidins, may help prevent bacteria from adhering to the lining of the urinary tract. But Dielubanza says the evidence is mixed, and she points out there's usually not enough concentration of the compounds in many of the sweetened cranberry juices sold in grocery stores to make a difference. So if you want to try it, some doctors suggest cranberry supplements instead.

Though there's less research to date, there's growing data supporting the use of another supplement, D-Mannose, a type of polysaccharide. Van Kuiken explains that D-Mannose gets rapidly excreted in urine. When bacteria bind to the polysaccharide, it can help flush them out of the urinary tract. "It's a safe supplement that's available over the counter," Van Kuiken says.

5. Approaching menopause and after, use vaginal estrogen cream

As the female body starts producing less estrogen during the years leading up to menopause, risk for UTIs can go up, says Dielubanza. "The loss of estrogen can change our vaginal microenvironment and make us more prone to developing UTIs," she says. "The good bacteria that colonize our vaginas may be less likely to survive after menopausal changes."

For women in perimenopause or later dealing with recurrent UTIs, some physicians advise starting some patients on topical vaginal estrogen.

"It amazes me how many women that I see that fall into this age category who have not heard of vaginal estrogen," says Van Kuiken. "Probably one of the single most important things that we can do to help prevent recurrent urinary tract infections is [prescribe] topical estrogen."

Editing and visuals research by Carmel Wroth. Audio editing by Jane Greenhalgh.