Abstract
Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.
Highlights
The global crisis of antimicrobial resistance (AMR) has been attributed to antimicrobial overuse, improper prescribing, extensive use as growth promoters in agriculture, and the slowing development of new antimicrobials [1]
As a result, filtering was conducted by using all results from the trip/extraction blank (TRBL)
Prior studies used ARDB and Resqu databases for antimicrobial resistance genes (ARGs) annotation for analysis [16,29]. Source material from these studies were lake sediment and sterile swabs of paper money, respectively, which likely contain less diverse Eukaryotic DNA contamination compared to food waste and compost samples; for example, when a single eukaryotic host can be identified those sequences can be filtered and removed, but this is an intensive process when dealing with an unknown number of plant genomes in composted materials
Summary
The global crisis of antimicrobial resistance (AMR) has been attributed to antimicrobial overuse, improper prescribing, extensive use as growth promoters in agriculture, and the slowing development of new antimicrobials [1]. Diversion of food scraps to agriculture is a sustainable practice, but in states such as Vermont it is being promoted as an alternative to meet current regulations. In the wake of Vermont’s Universal Recycling Law (Act 148) [2] and similar legislation in other states or municipalities, the fate of microbial species in food waste and residuals is under scrutiny; agricultural composts and soils represent a major contact point between the environment, animals, and humans, yet the extent of novel bacteria and associated antimicrobial resistance genes (ARGs) in comingled food residuals is unknown. Poultry farms may represent increased risk, as in contrast to the regulation of feeding of food waste to species such as swine, in Vermont there are no prohibitions on using raw food scraps as poultry feed[3]
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