The food-associated resistome is shaped by processing and production environments

Area of Science:

• Microbiology
• Food Science
• Genomics

Background:

• Food production systems can transmit antimicrobial-resistant bacteria and genes to humans.
• The food resistome, encompassing all antimicrobial resistance genes (ARGs) in food, is not well understood.

Purpose of the Study:

• To characterize the food resistome across various food production stages.
• To identify the prevalence and types of ARGs in food production environments.
• To determine the bacterial hosts and mobile genetic elements associated with ARGs in food.

Main Methods:

• Whole-metagenome sequencing of 1,780 samples from raw materials, end-products, and surfaces in 113 food processing facilities.
• Assembly-free and assembly-based analyses to identify ARGs and their carriers.
• Evaluation of ARG association with mobile genetic elements.

Main Results:

• Over 70% of known ARGs were detected in food production chains, including those conferring resistance to critical antibiotics.
• Tetracyclines, β-lactams, aminoglycosides, and macrolides resistance genes were most abundant.
• ESKAPEE group bacteria, Staphylococcus equorum, and Acinetobacter johnsonii were primary ARG carriers.
• ~40% of ARGs were linked to mobile genetic elements, primarily plasmids.

Conclusions:

• The food resistome is extensive and harbors numerous ARGs, posing a potential risk for human exposure.
• Understanding ARG carriage and mobility in food production is crucial for developing effective antimicrobial stewardship policies.
• Findings support targeted interventions in food production to mitigate the spread of antimicrobial resistance.