Thirty years of Monitoring Antibiotic-Resistant Bacteria in the United States, and Over a Decade of FSIS Contributions

Thirty years of Monitoring Antibiotic-Resistant Bacteria in the United States, and Over a Decade of FSIS Contributions

By Uday Dessai, Gamola Fortenberry, Catherine Rockwell, Jovita Haro, Doug Noveroske, Andrea Cote and Bonnie Kissler

USDA Food Safety and Inspection Service

Antimicrobial resistance (AMR) occurs when bacteria and other microorganisms adapt in ways that make medicines less effective. When this happens, infections can become harder to treat and more likely to spread. According to estimates from the Centers for disease Control and Prevention (CDC), AMR infections affect millions of people in the U.S. each year and contribute to thousands of deaths.

To better understand and respond to this growing challenge, USDA, CDC, and the Food and Drug Administration (FDA) came together in 1996 to establish the National Antimicrobial Resistance Monitoring System (NARMS). Today, NARMS is a partnership between the three federal agencies and state and local public health agencies. Together, these partners monitor AMR in people, retail meat products, and food-producing animals to better understand how resistance emerges and spreads.

FSIS has played a major role in strengthening and modernizing this work over the past decade. The Agricultural Research Service (ARS) originally led NARMS activities at USDA. ARS helped establish the scientific foundation for AMR surveillance in food-producing animals. In 2013, the program transitioned to FSIS, where the agency expanded surveillance efforts and integrated this work more directly into food safety decision-making.

Since then, FSIS has worked closely with FDA and CDC to modernize and expand AMR data collection, analysis, and information sharing. Together we expanded susceptibility testing for important foodborne pathogens such as Salmonella and Campylobacter, and increased surveillance of indicator organisms such as E. coli and Enterococcus sp. These efforts helped NARMS scientists to better understand nation-wide resistance trends in food animals before they enter the food supply. At this time, newer technology called whole genome sequencing (WGS) was developing rapidly. FSIS worked with NARMS partners to apply this cutting-edge technology to NARMS surveillance. FSIS also rapidly built high-throughput capacity and the necessary expertise for routine application of WGS in food safety and public health, and shortly thereafter became a leader in the high-throughput WGS field.

WGS is a scientific method that reveals the genome/DNA of a pathogen with great detail, including the genes responsible for antimicrobial resistance. Using WGS, we can determine how certain bacteria are related to other bacteria recovered from food, environmental and clinical samples from sick people. To use WGS data effectively, it should be available rapidly and freely for conducting in-depth and comprehensive epidemiologic or AMR analysis. For unhindered access, WGS data must be uploaded and stored in universally accessible databases, such as the National Center for Biotechnology. FSIS became the first high-throughput laboratory system to publicly share this type of sequencing data in near real-time, helping researchers and public health partners identify emerging resistance patterns faster. Once complete, analyses are uploaded to national WGS databases at CDC PulseNet and the National Center for Biotechnology.

During certain years, FSIS expanded NARMS sampling to include additional animal species such as goats, sheep, lamb, veal, and Siluriformes fish and cattle lymph nodes, providing a broader national picture of AMR across the U.S. food system. FSIS NARMS data have helped investigators better understand and respond to foodborne illness outbreaks linked to AMR strains of Salmonella, including the Reading and Infantis serotypes. In both cases, FSIS' NARMS data from intestinal and product samples helped connect the preharvest origin and geographic distribution of these serotypes to tailor outbreak responses. Today, FSIS routinely uses NARMS data to support food safety decisions, identify emerging concerns, inform stakeholders, and strengthen prevention strategies across the food supply.

As we look back on 30 years of NARMS, this partnership remains one of the nation's most important systems for tracking the naturally occurring biological threat of AMR. By monitoring, preventing, and responding to early trends, NARMS is a testament of successful interagency coordination. FSIS' role in modernizing surveillance, expanding sampling, improving analytics, and enhancing the timeliness of data sharing has strengthened the nation's ability to protect public health by promptly detecting and responding to AMR or other emerging threats.