Cow manure harbors diverse new antibiotic resistance genes

Manure from dairy cows, which is commonly used as a farm soil fertilizer, contains a surprising number of newly identified antibiotic resistance genes from the cows' gut bacteria.

The findings, reported in mBio the online open-access journal of the American Society for Microbiology, hints that cow manure is a potential source of new types of antibiotic resistance genes that transfer to bacteria in the soils where food is grown.

Thousands of antibiotic resistance (AR) genes have already been identified, but the vast majority of them don't pose a problem when found in harmless bacteria. The real worry is when these genes appear in the types of pathogenic bacteria that cause food-borne illnesses or hospital infections.

"Since there is a connection between AR genes found in environmental bacteria and bacteria in hospitals, we wanted to know what kind of bacteria are released into the environment via this route," of manure fertilization, says Fabienne Wichmann, lead study author and former postdoctoral researcher at Yale University in New Haven, Connecticut.

Farmers use raw or composted cow manure on some vegetable crops, which could lead to a scenario where residual manure bacteria might cling to produce and they or their genes might move to the human ecosystem. "Is this a route for movement of these genes from the barn to the table?" asks Jo Handelsman, senior study author and microbiologist at Yale.

Handelsman's team used a powerful screening-plus-sequencing approach to identify 80 unique and functional AR genes. The genes made a laboratory strain of Escherichia coli bacteria resistant to one of four types of antibiotics—beta-lactams (like penicillin), aminoglycosides (like kanamycin), tetracycline, or chloramphenicol.