The purpose of this study was to assess the antimicrobial resistance gene (ARG) and mobile genetic element (MGE) gene presence and abundance in soil, dairy manure and plant mixed compost (DMP), plant-based compost (P), and gardeners who used DMP across three time points. Soil (n = 1), DMP (n = 1), P (n = 1), and participant (n = 11) stool samples were collected at three time points during the 2019 gardening season in the Lansing, MI, area. DNA was extracted from each sample and stored at -20°C until use. Quantitative real-time PCR was used to detect ARGs and MGEs in each sample. Alpha diversity was assessed using richness, Shannon, and inverse Simpson indices. Shapiro-Wilk tests were used to assess normality. Beta diversity was assessed using Sorensen and Bray-Curtis dissimilarity indices. We detected a diverse composition of ARGs and MGEs in soil, compost, and human stool samples. DMP and soil exhibited greater ARG richness than P compost. In human stool, ARG and MGE profiles showed inter-participant variability but remained largely consistent within individuals across the gardening season. Alpha and beta diversity metrics revealed no significant shifts in the overall human gut resistome diversity across the gardening season. However, MGE gene composition differed significantly between DMP compost and human stool samples. Although ARG and MGE were detected in the soil and compost samples, there was no change in the ARG and MGE composition of gardeners' gut resistomes over the gardening season. These findings suggest that short-term exposure to AMR-rich compost or soil may not substantially alter gut resistome structure in healthy adult populations.
Importance: Antimicrobial resistance is a growing public health concern, and compost and soil can contain genes that help bacteria resist antibiotics or share resistance with other bacteria. Many gardeners use manure-based compost, but it is unclear whether short-term exposure affects antimicrobial resistance in bacteria residing within the human gut. In this study, we detected antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in soil, two types of compost, and stool from gardeners across the 2019 gardening season near Lansing, MI. We found that manure-based compost and soil contained more ARGs than plant-based compost, but gardeners' gut resistomes remained stable over time. These results suggest that short-term compost exposure through gardening may not substantially alter the gut resistome.
Keywords: antimicrobial resistance; bacteria; compost; gardening; human; microbiome; resistome; soil.