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

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 β-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 β-lactams were in highest relative abundance (RA) on cold-stored lettuce and lowest in soil. Several extended-spectrum β-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 β-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.