Cow manure harbours antibiotic resistance genes

Manure from dairy cows, which is commonly used as a farm soil fertiliser, contains a surprising number of genes that can fuel resistance to antibiotics, a new study has warned.
The findings suggest that cow manure is a potential source of new types of antibiotic resistance (AR) genes that transfer to bacteria in the soils where food is grown.
"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 fertilisation," said 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?" asked Jo Handelsman, senior study author and microbiologist at Yale.
The first step toward an answer was surveying which AR genes are present in cow manure. 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.

Roughly 75 per cent of the 80 AR genes had sequences that were only distantly related to AR genes already discovered.
The team also found an entire new family of AR genes that confer resistance to chloramphenicol antibiotics, which are commonly used to treat respiratory infections in livestock.
"The diversity of genes we found is remarkable in itself considering the small set of five manure samples. But also, these are evolutionarily distant from the genes we already have in the genetic databases, which largely represent AR genes we see in the clinic," Handelsman said.
That might signal good news that AR genes from cow gut bacteria are not currently causing problems for human patients.

But, Wichmann pointed out, another possibility is that "cow manure harbours an unprecedented reservoir of AR genes" that could be next to move into humans.
AR genes can enter the human ecosystem by two routes - either the bacteria that contain them colonise humans, or the genes are transferred through a process called horizontal gene transfer to other bacteria that colonise humans.
The study is published in the journal of the American Society for Microbiology.