Urban farming is becoming an increasingly important implement in the toolbox for fighting food insecurity and bringing nutritious food into many underserved communities. But soils in urban settings are often contaminated with the build-up of human waste products, including pathogens and bacteria that have developed resistance to antimicrobial products.

New work by researchers from the College of Agriculture & Natural Resources (AGNR) at the University of Maryland (UMD) shows why it is important to understand and monitor antimicrobial-resistant bacteria and their genes in urban farm soils to reduce the risks in the food system. 

The study was coauthored by Ryan Blaustein, an assistant professor of nutrition and food science and member of the UMD Center of Excellence in Microbiome Sciences. His team includes Erin Harrelson and Qingyue Zeng, both Ph.D. students in Nutrition and Food Science; Postdoctoral Associate Mairui Gao; and Magaly Toro, an associate research professor in AGNR who directs the Joint Institute of Food Safety and Applied Nutrition.

Published in the journal Frontiers in Plant Science, the research describes the presence of antimicrobial-resistant genes in harmless soil microbes that have the potential to find their way into pathogens that can infect people.

Antimicrobial resistance (AMR) contributes to an estimated 2.8 million infections and over 35,000 deaths annually in the U.S. Much of the focus on reducing agriculture’s role in spreading AMR has been directed at reducing antibiotic use in animal production. But very little is known about AMR bacteria in urban soils and how AMR-resistant genes move through urban agricultural environments.

Blaustein’s previous work showed that urban soils treated with organic material—such as compost and treated manure—had lower proportions of ampicillin- and tetracycline-resistant bacteria compared to native soils. That was an encouraging finding that suggested soil amendments might shift the microbial community, adding good microbes to mitigate or dilute populations of AMR microbes.

But Blaustein and his colleagues also found a high level of multi-drug resistance. Meaning among the antimicrobial resistant microbes in their samples—which came from soils and leafy green vegetables like kale and lettuce from seven urban farms and community gardens around Washington, D.C.—many were resistant to multiple antibiotics. Multi-drug resistance, or MDR is particularly concerning because pathogens with this trait can become difficult to treat with available medications. In recent years, MDR pathogens such as MRSA and Candida auris have become an increasingly deadly public health threat.

Blaustein’s team wanted to know what kinds of microbes were developing multi-drug resistance in urban farm environments and what level of threat they may pose to public health.

In their recent work, they sequenced the whole genomes of bacteria collected during their earlier study that showed resistance to multiple antibiotics. Their results revealed that many types of bacteria contained MDR genes, but none were common foodborne pathogens. That finding was reassuring; however, the researchers identified a concerning trait. Many of the drug-resistant genes were located very close to gene signatures for small, mobile sections of DNA called plasmids. These plasmids can be transferred between bacteria, which means under the right conditions, antibiotic-resistant genes could be transferred too.

Although the multi-drug-resistant bacteria Blaustein and his team found in urban farm environments are not thought to pose direct threats to human health, they could serve as a reservoir for multi-drug-resistant genes that may one day jump into pathogenic bacteria in the food system, such as E-coli or salmonella. These results highlight the importance of Blaustein’s work.

“Overall, the food safety risk from antimicrobial resistance in urban agriculture is low,” Blaustein said, “but the potential for anti-resistance genes to move through the system represents an emerging concern that we and others need to be watching out for.”

—Story by Kimbra Cutlip, College of Agriculture & Natural Resources