Metagenomic characterization of the antibiotic, biocide, and metal resistome of soil and romaine lettuce from the field through processing and storage

Authors: LEONARD, SUSAN - Food And Drug Administration(FDA); MAMMEL, MARK - Food And Drug Administration(FDA); RICHTER, TAYLOR - Food And Drug Administration(FDA); Simko, Ivan; Brandl, Maria

Submitted to: International Journal of Food Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2025
Publication Date: 12/22/2025
Citation: Leonard, S., Mammel, M., Richter, T., Simko, I., Brandl, M. 2025. Metagenomic characterization of the antibiotic, biocide, and metal resistome of soil and romaine lettuce from the field through processing and storage. International Journal of Food Microbiology. 448:111595. https://doi.org/10.1016/j.ijfoodmicro.2025.111595.
DOI: https://doi.org/10.1016/j.ijfoodmicro.2025.111595

Interpretive Summary: The rise of antimicrobial resistance jeopardizes our ability to treat infectious diseases and is causing a global public health crisis. The presence of antimicrobial resistance genes on crops is of concern to human health since plant-derived foods may serve as their vectors to human pathogens. This study mined the microbial metagenomes of soil and lettuce from harvest through processing and storage to characterize their comprehensive resistomes, which encompass all genes encoding resistance to antibiotics, metals, and biocides. Genes for resistance to copper, mercury and multi-metal resistance were predominant in most comprehensive resistomes. Cold-stored lettuce had a significantly greater number of resistance genes than soil at harvest, lettuce heads at harvest, and processed lettuce (cut and chlorine-washed) before storage. Lettuce processing enriched heavily for biocide resistance genes. Drug resistance genes in cold-stored lettuce were dominated by those encoding resistance to the beta-lactams class of antibiotics, which were detected in greater relative abundance in the microbial metagenome of spring- than fall-harvested lettuce, and of lettuce from the commercial than experimental field.

Technical Abstract: The presence of antimicrobial resistance genes (AMRGs) on crops is of concern to public health since plant-derived foods may serve as vectors of AMRGs to human pathogens. This study mined the bacterial metagenomes of soil and lettuce from harvest through processing and storage to characterize their comprehensive resistomes (antibiotics, metals, and biocides). Cold-stored lettuce had the greatest number of AMRG reads per million of all sample types. AMRGs were overall dominated by metal resistance determinants, except those of processed lettuce (cut, washed in chlorinated water, and rinsed), which were heavily enriched in genes encoding biocide resistance. The greatest percentage of drug resistance genes, when averaged over all sample types, belonged to resistance to ß-lactams (30%) followed by aminoglycosides (6.7%), and specific allele sequences from both classes were observed in common between lettuce and soil sampled next to lettuce heads. Genes for resistance to ß-lactams were in highest relative abundance (RA) on cold-stored lettuce and lowest in soil. Several extended-spectrum ß-lactamase genes and the colistin resistance gene mcr-9.1 were detected in the cold-stored lettuce resistome. Harvest season and field type had a significant effect on the comprehensive resistome of most sample types (PERMANOVA, P < 0.05). Notably, the RA of ß-lactams resistance genes in the drug resistome of cold-stored lettuce represented 17.4% and 2.0% in spring vs. fall, and 11.3% and 3.9% in the commercial vs. experimental field, respectively. This study highlights the multifactorial role of the biotic and abiotic environment on the comprehensive resistome of lettuce during production and storage.