A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle.

Area of Science:

• Veterinary Microbiology
• Food Safety
• Genomics and Bioinformatics

Background:

• Foodborne pathogens present significant health risks and economic burdens in the U.S.
• Antimicrobial resistance (AMR) in these pathogens is a growing global concern.
• The National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) offers a valuable resource for AMR data.

Purpose of the Study:

• To conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the last decade.
• To identify predominant pathogens and prevalent AMR genes associated with cattle in the U.S.
• To track trends in AMR gene occurrence and geographic distribution.

Main Methods:

• Analysis of approximately 28,000 pathogen isolates from the NPDIB.
• Application of multivariate statistical methods, including Principal Component Analysis (PCA) for data dimension reduction and Hierarchical Clustering (H-clustering) for data point differentiation.
• Identification of specific AMR genes and antimicrobial resistance patterns.

Main Results:

• *Salmonella enterica* and *Escherichia coli* were identified as the most prevalent pathogens, with *E. coli* showing increasing prevalence.
• Tetracycline emerged as the most common antimicrobial resistance, associated with genes like *mdsA*, *mdsB*, *mdtM*, *blaEC*, and *acrF*.
• An increasing occurrence of *mdtM*, *blaEC*, *acrF*, and *glpT_E448k* was observed in recent years. Texas, California, and Nebraska were identified as key geographic areas with significant AMR gene prevalence.

Conclusions:

• *E. coli* and *Salmonella* in U.S. cattle are significant reservoirs for AMR genes.
• The rising prevalence of specific resistance genes and tetracycline resistance highlights an urgent need for monitoring and intervention.
• Geographic hotspots for AMR in cattle necessitate targeted control strategies to mitigate public health risks.