Animal microbiome researcher awarded $1.3M to study pathogenic threats

UNIVERSITY PARK, Pa. — Erika Ganda, assistant professor of food animal microbiomes and executive committee member of Penn State’s One Health Microbiome Center, was recently awarded two grants totaling $1.3 million from the U.S. Department of Agriculture (USDA) to lead teams of scientists in the College of Agricultural Sciences and Penn State Extension in studies of pathogenic threats to livestock and people.

The grants from USDA’s National Institute for Food and Agriculture will fund Ganda’s teams as they investigate the links between harmful microbes and animal and human health.

In the first project, the Ganda Lab — which focuses on animal microbiomes and the One Health vision, an integrated, unifying approach that aims to sustainably balance and optimize the health of people, animals and ecosystems — plans to devise and test a comprehensive and cost-effective method to understand the impact of feed additives on antimicrobial resistance. A $1 million grant is funding this research.

A threat to human and animal health, as well as the food supply, antimicrobial resistance is often transmitted from animals to humans, Ganda pointed out.

“While the link between antimicrobial use and the rise of antimicrobial resistance transmission has been established, specific agricultural practices that may mitigate the transmission of antimicrobial resistance are yet to be identified,” she said. “To generate the antimicrobial resistance transmission data needed to identify such practices and support evidence-based antimicrobial stewardship, a comprehensive and cost-effective antimicrobial resistance transmission surveillance method is critically needed.”

The existing techniques used for tracing antimicrobial resistance transmission mostly rely on isolate-based testing, which is time-consuming and provides information on only a few pathogens and antibiotics, Ganda explained. Another limited approach is to DNA sequence microbial communities in a sample using a comprehensive technique, known as culture-independent shotgun metagenomics, to gather a comprehensive profile of the antimicrobial resistance landscape.

However, this method is prohibitively expensive to broadly apply for surveillance, she noted.

“The goal of our awards is to refine, validate, apply and disseminate an antimicrobial resistance-profiling method developed by our group — which we call rhAMR.” Ganda said. “By adapting highly multiplexed amplicon sequencing-based technologies, we will gather information on thousands of antimicrobial-resistance variant genes of interest with same-day results. This rapid deployment and scaling for detection of antimicrobial resistance will be a game changer for industries such as diagnostics, animal and human health, and biotech that we hope to collaborate with in the near term.”

The researchers said they plan to validate rhAMR in collaboration with an external laboratory, and then apply rhAMR to compare the effect of different feeding strategies on antimicrobial resistance. The team plans to develop curricula and extension training on monitoring and mitigation of antimicrobial resistance in the food supply chain and offer technology-transfer activities to facilitate the adoption of rhAMR by others.

Along with project co-investigators Jasna Kovac, the Lester Earl and Veronica Casida Career Development Professor of Food Safety, and John Boney, the Vernon E. Norris Faculty Fellow of Poultry Nutrition, Ganda said she intends to apply the refined method to answer a biologically relevant question: What is the impact of different alternatives to antibiotic feed additives on antimicrobial resistance in broiler production? Broilers are chickens raised for meat.

“We know that by feeding higher levels of copper and zinc, which are not antibiotics, we still see rises in antimicrobial resistance because the bacteria have similar mechanisms to resist metals and antibiotics,” Ganda said. “There is very limited data on what the impact of feeding essential oils, prebiotics and probiotics have on antimicrobial resistance. We aim to help fill that gap.”

In the second project, funded by a $300,000 grant, Ganda and her colleagues will work with farmers to develop mitigation methods to deal with Salmonella Dublin, an emerging pathogen in dairy farms in the U.S. Northeast.

The pathogen is adapted to cattle and can also infect humans, she noted, adding that it is “a poster child of a One Health issue,” since it can persist on farms for months to years, can be extremely difficult to treat due to its multi-drug resistance, and can be transmitted from animals to humans.

“This strain is slowly increasing in prevalence across the United States and can result in severe economic loss,” Ganda said. “However, no data are available regarding the herd prevalence of Salmonella Dublin in Pennsylvania dairy herds, despite this pathogen being isolated from several human cases in Pennsylvania since 2014 and many animal cases in the past two years.”

This project aims to address the potentially underdiagnosed problems caused by Salmonella Dublin in the Pennsylvania dairy industry. Researchers plan to screen bulk tank milk samples for Salmonella Dublin antibodies to determine how widespread the pathogen is. For positive herds, the researchers plan to offer to work with farmers and use advanced-detection methods to isolate the bacteria from animals and the environment in a "seek and destroy" approach, Ganda said.

“We will also use a structured risk-assessment tool to evaluate farms and identify major points of transmission to create a tailored mitigation approach in each herd,” Ganda said.

The team said they will develop a suite of extension resources to increase the level of knowledge about Salmonella Dublin, and to change attitudes and behaviors toward the prevention, detection and control of Salmonella in dairy herds. Researchers plan to leverage the extensive reach of Penn State Extension to provide educational resources for Pennsylvania dairy farm owners and employees, as well as the veterinarians who work with these dairy farms.

“These resources and engagement opportunities will increase knowledge and positively impact attitudes and behaviors about preventing and controlling Salmonella Dublin in dairy herds and reducing the risk of zoonotic disease,” Ganda said. “Ultimately, that will lead to improved management and biosecurity in Salmonella Dublin-positive herds in Pennsylvania.”

Team members include Ernest Hovingh, research professor and resident director of Penn State’s Animal Diagnostic Lab and extension veterinarian; Adrian Barragan, associate research professor and extension veterinarian; and Hayley Springer, associate clinical professor and extension veterinarian. They are actively recruiting farms interested in having their bulk tank milk tested for free.