Assessment of a monitoring program of pig farms' antimicrobial purchase and resistance monitoring program for Escherichia coli and Salmonella enterica in the Midwestern United States, May 2020 through October 2023

Karyn Havas^1*Roy Edler¹Laura Ruesch²Marlee Braun²Peter Ferm³Noelle R Noyes³Laura B Goodman⁴Harvey Morgan Scott⁵Joel Nerem⁶Taylor Spronk⁶Scott A Dee¹

• ¹Pipestone Research, Pipestone, United States, Pipestone, Minnesota, United States
• ²Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, United States
• ³Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States
• ⁴Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States
• ⁵Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University College Station, College Station, Texas, United States
• ⁶Pipestone Veterinary Services, Pipestone, United States

Antimicrobial resistance (AMR) challenges health and treatment options in human and veterinary medicine. Animal AMR monitoring in the US evaluates carcasses, retail meat, live animals, and diagnostic laboratory submissions, but there is a lack of consistent on-farm monitoring of use and resistance. In 2020, 153 pig farms in the Midwestern United States enrolled in an antimicrobial purchase and resistance monitoring program. Intestinal samples or fecal swabs were collected biannually for three years from pigs and their dunging areas; antibiotic purchase data were tracked. Salmonella enterica and Escherichia coli were isolated and underwent antibiotic susceptibility testing using either a commercial bovine/porcine (BOPO 7F) panel (pig samples) or the National Antimicrobial Resistance Monitoring System (NARMS) gram negative panel (dunging area samples). Minimum inhibitory concentrations (MIC) of antibiotics were used to evaluate susceptibility of pig sample isolates while NARMS breakpoints were used to determine resistance for the dunging area isolates. Tetracylines were the most purchased and penicillins the most used antibiotic class across farm types. For pig samples, more isolates exhibited MIC values at the high end of the tested range among E. coli and Salmonella isolates from wean-to-market (WTM) sites compared to breed-to-wean (BTW) sites for almost all antibiotic classes. In addition, E. coli isolates from sick pigs had higher MIC values compared to isolates from substandard but otherwise healthy pigs. Among, the dunging area isolates both bacteria had higher rates of resistance in the WTM sites compared to the BTW sites across multiple antibiotics. Individual ages of pigs were a likely confounder and were not controlled for since these data were not reliably collected. Greater frequency of monitoring, as well as controlling for age, recent treatments, and disease events at an individual-level would improve farm-level insights from on-farm AMR monitoring. Currently, interpretation of phenotypic AMR data for resistance monitoring in swine medicine is limited by the lack of established veterinary breakpoints for enteric organisms. The NARMS breakpoints available are for humans and can be used for public health monitoring and are likely to be mostly valid for gastrointestinal infections involving the same bacteria in farm animals.