NIH grant: Expanding Vet-LIRN Antimicrobial Resistance Surveillance through Phenotypic Testing and Whole Genome Sequencing (1U18FD008945-01)

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NIH grant 1U18FD008945-01: Expanding Vet-LIRN Antimicrobial Resistance Surveillance through Phenotypic Testing and Whole Genome Sequencing
Institute: {'code': 'FD', 'abbreviation': 'FDA', 'name': 'Food and Drug Administration', 'admin_org_id': '12500799', 'admin_funding_url': ''}. PI: Ailam Lee Lim. Award: $57714.
Start: 2026-09-25T00:00:00.
Project Abstract
 Foodborne bacterial pathogens and antimicrobial resistance (AMR) pose an escalating
threat to animal and public health, resulting in substantial morbidity, mortality, and economic
burden in the United States. Priority foodborne pathogens including Salmonella, Escherichia
coli, Campylobacter spp., and Listeria monocytogenes are responsible for millions of human
illnesses annually and are frequently recovered from livestock and companion animals. The
emergence and spread of antimicrobial-resistant strains among these pathogens further
reduce treatment options and increase the risk of zoonotic transmission at the animal-human
interface. These risks are compounded by the increasing popularity of raw pet food diets,
underscoring the need for coordinated AMR surveillance within a One Health framework.
 This proposal directly supports the objectives of PAR-23-202 by strengthening
antimicrobial resistance monitoring within the FDA Veterinary Laboratory Investigation and
Response Network (Vet-LIRN). Leveraging the diagnostic capacity and technical expertise of
the Wisconsin Veterinary Diagnostic Laboratory (WVDL), this project will expand Vet-LIRN
AMR datasets through standardized phenotypic and genotypic characterization of animal-
derived bacterial pathogens. WVDL maintains hundreds of isolates already characterized
through fee-for-service diagnostics and National Animal Health Laboratory Network (NAHLN)
AMR funded activities using broth microdilution methods in accordance with Clinical and
Laboratory Standards Institute (CLSI) guidelines. This project will extend these efforts by
profiling additional clinically and epidemiologically relevant isolates recovered from companion
animals.
 Specifically, we will (1) determine phenotypic antimicrobial resistance profiles for
additional 100 E. coli, Salmonella, Campylobacter spp., and L. monocytogenes isolates from
diverse animal hosts, and (2) generate high-quality whole genome sequences for up to 200
selected isolates exhibiting clinically significant resistance patterns using the Illumina MiSeq
i100 platform. Sequencing data will undergo standardized bioinformatic analysis and be
deposited into the Vet-LIRN database.
 By integrating antimicrobial susceptibility testing with whole genome sequencing, this
project will strengthen national AMR surveillance capacity, support outbreak detection and
response, and directly advance Vet-LIRN’s mission to protect animal and human health
through improved antimicrobial stewardship and food safety preparedness.

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