One of the most common and troubling infections that occur in healthcare may come from an unexpected source, according to a new paper: from food. Yet because it is not one of the bacteria that we think of as disease-causing foodborne organisms, the size of the threat it poses, and the way it reaches us, may not be well understood.

The infection is Klebsiella pneumoniae, a stubborn gut-dwelling organism that can cause pneumonia, bloodstream infections and meningitis. The finding that it is present in food—and in some cases, practically genetically identical in food and in hospitals—comes from a multi-institute project that for several years has been closely analyzing pathogens found on supermarket meat and in hospital patients in Flagstaff, Ariz. The collaboration chose Flagstaff because it is home base for the institution that started the study, the private Translational Genomics Research Institute (TGen), and also because it is a relatively isolated city with one major medical center and a small number of grocery store chains, which put useful boundaries on a project looking at bacterial traffic between medical settings and food.

“We’re trying to understand what kind of infections food can convey,” Lance Price, PhD, a molecular biologist and the senior author of the study, told me. “And in this case, we see pretty compelling evidence that food can serve as a source of exposure to Klebsiella, one of the most important opportunistic pathogens in the United States.”

Klebsiella enters hospitals in the guts of unknowing patients, and like other pathogens that cause serious hospital-acquired infections, escapes their guts when multiple courses of antibiotics and other drugs cause diarrhea. Fine particles can contaminate the air and hard surfaces in hospital rooms, and then are transferred back to the patient, or to other patients, by hands—their own, or a health care worker’s—or by equipment. Klebsiella increasingly is also highly drug resistant, and the Centers for Disease Control and Prevention rank the most resistant form as an “urgent” health threat requiring immediate national action.

But just where Klebsiella comes from, in order to make it into patients in the first place, has been a bit of a mystery—as well as a less important question for research than what happens once it causes an infection. “We tend to think of this organism as being one that individuals carry naturally, or acquire from the environment,” said James Johnson, MD, a co-author and professor of medicine at the University of Minnesota and Minneapolis VA Healthcare System.

Johnson and Price are long-time collaborators on studies of E. coli, another disease organism that contaminates hospital environments, unpredictably causes severe illness, and travels on food. They hypothesized Klebsiella might behave in the same way. For this study, they and the rest of the team—from TGen; George Washington University, where Price heads the Antibiotic Resistance Action Center; and institutions in Flagstaff, Baltimore and Denmark—looked for the bacterium in 508 packages of chicken, turkey and pork bought in Flagstaff supermarkets over 10 months, and in 1,728 samples of blood or urine taken from Flagstaff hospital patients during the same time span.

They found that 10 percent of the patients, and 47 percent of the meat, carried Klebsiella. Moreover, 22 percent of the Klebsiella—32 percent of those found on meat and 8 percent of those found in patients—were multi-drug resistant, that is, to at least three different families of antibiotics. When they put the samples from meat and from patients through MLST, an analysis that groups organisms into types on the basis of similarities in certain genes, they found that the meat and human isolates were not different, but fell into the same types. And when they sequenced the entire genomes of a randomly chosen subset of the Klebsiella from each source, and then compared them to see how alike or different they were, they found that the meat-source and human isolates did not separate out, but clustered within groups. Of the 38 human-source isolates they chose for close scrutiny, 5—13 percent—were almost identical to ones that came from meat. When they used those matched pairs to infect mice experimentally, the human-origin and meat-origin bacteria were equally virulent.

So what does this mean? Price said in a phone conversation that the results show how limited our awareness of foodborne organisms is. Public concern, and public-health surveillance, focus on well-known pathogens such as Salmonella and Campylobacter where the link between food consumption and illness is more evident, but discount bacteria that do not cause immediate illness, That suggests, first, that foodborne illness is more widespread than we detect, and given the sometimes fatal illness that Klebsiella causes, more serious as well.

But an additional, crucial issue, revealed by the results and by additional testing done on the different groups of bacterial samples, is the influence of antibiotics that are given to meat animals. The resistance patterns in the Klebsiella isolated from humans were not all like each other, and the resistance patterns in meat were not all alike either; but certain samples taken from humans matched samples in the meat-source pool. That suggests, Price said, that the bacteria did not all enter the local hospital and become resistant there due to homogeneous patterns of drug use in the medical center. Instead, the bacteria became differently resistant depending on the degree of antibiotic use on the farms where animals were raised, and then passed that idiosyncratic pattern to whichever human consumed the meat the animal became.