Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

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.

The development of the oral resistome during the first decade of life

“…Three ARGs -aph6'Id, tet(W) and tetA (60) were consistently signi cantly more abundant in the healthy resistome compared to caries (CA), as severity of the disease progressed. The aminoglycoside gene aph6'Id is a known resident on MGEs and is capable of expression in a variety of bacterial species which may explain why it persists in the healthy resistome 43 . Two ARGs, blaOXA-85 and catP persisted as the disease progressed suggesting that these genes may be linked with caries associated microbiota.…”

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

“…Shotgun whole-metagenome sequencing (WMS) is a reliable tool that can provide a comprehensive and high-resolution analysis of the microbiome and resistome ( Schmieder and Edwards, 2011 ; Nesme et al, 2014 ; Ghanbari et al, 2019 ; Ma et al, 2021 ), and it has been applied to quantify the abundance of many resistance genes in parallel in poultry ( Wang et al, 2017 ; Kumar et al, 2020 ), cattle ( Thomas et al, 2017 ), pig ( Ghanbari et al, 2019 ; Mencía-Ares et al, 2020 ) and the human gut ( Feng et al, 2018 ). Other metagenomic studies have found multiple ARGs in chicken gut as well ( Tong et al, 2017 ; Xiong et al, 2018 ; Eckstrom and Barlow, 2019 ; Wang Y. et al, 2021 ; De Cesare et al, 2022 ). However, WMS provides only limited information regarding ARG activity or the overall functional profile of the active microbial community.…”

Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

“…Specific feed blends for poultry are designed to promote the health and growth of birds. Before regulatory and market force changes were activated, these blends often contained arsenic [ 10 , 35 ] and/or veterinary antibiotic residues [ 36 ]. Heavy metals, antibiotics, and human pathogens pass intact through the digestive system to the fecal material [ 35 , 36 ], which represents a portion of poultry litter.…”

“…We have no direct evidence that either PLC or DMC contained antibiotic resistance genes (ARG) despite the presence of genera associated with ARG. In addition, the composting process is demonstrated to mitigate the persistence of ARG [ 10 ].…”

“…There is an increasing trend to feed food waste to poultry as a means to divert edible material to a useful purpose prior to sending it to a landfill or composting [ 9 ]. Food waste may contain bacteria known as human pathogens that may harbor antibiotic resistance genes or other contaminants, including heavy metals [ 10 ]. Agricultural composts and soils represent a major contact point between the environment, animals, and humans.…”