PhD candidate Ilya Slizovskiy, DVM, MPH, is the recipient of a new fellowship created by the U.S. Department of Agriculture’s Food Safety Inspection Service, FSIS. The competitive fellowship is committed to data-driven and science-based approaches applied to all aspects of FSIS public health mission. Slizovskiy’s project focuses on new techniques to detect antimicrobial resistances and foodborne pathogens.

Each year, 1 in 6 Americans suffer an illness from foodborne hazards, and these food-related illnesses cost the U.S. economy more than 50 billion dollars annually. The U.S. Department of Agriculture (USDA) Food Safety Inspection Service in collaboration with the Food and Drug Administration (FDA) and Centers for Disease Control and Prevention (CDC), aim to reduce new cases of foodborne illness and prevent rise in foodborne infections resistant to certain antibiotics. Pathogens with antimicrobial resistance can cause more serious health outcomes and are more expensive to treat.

Currently, regulators rely primarily on methods requiring microbial culture and phenotyping to profile specific pathogens and antimicrobial resistance in samples. However, such culture-based techniques are unable to capture a vast proportion of microbial genetic diversity, some of which likely has public health and clinical importance. 

With guidance and support from his PhD advisor, Noelle Noyes, DVM, PhD, Ilya will collaborate with USDA scientists to deploy scalable novel metagenomic sequencing approaches developed at the Noyes Lab, in order to detect > 7,000 critical antimicrobial resistance genes, > 5,000 mobile genetic elements, > 6,000 virulence factors, and four priority foodborne pathogens in samples collected during surveillance and outbreak investigations. 

This project is supported by an inaugural fellowship recently instituted in partnership with the FDA and CDC to mitigate spread of antimicrobial resistance (AMR) throughfood systems. The fellowship is developed to help address goals of the Healthy People 2030 initiative (U.S. Department of Health and Human Services), and initiatives to modernize inspection systems through the 2020 Roadmap to Reducing Salmonella (USDA).