High copy number of multi-drug resistance genes in spent coffee grounds used in organic composting

Abstract

Background: The demand for organic composts made of animal manure and food waste, such as spent coffee grounds, is increasing as organic farming is gaining popularity. One of the potential public health hazards of using these organic composts is the dissemination of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Animal manure is generally believed to be the primary source of these bacteria and genes since antibiotics are commonly used in animal farming. However, there is little concrete evidence supporting this claim. Here, we examined this argument by characterising the resistome of the raw materials, namely, chicken manure (CF), spent coffee grounds (COFFEE), and chopped grass (GRASS) commonly used in Hong Kong for preparing organic composts. Methods: Three independent samples of the three raw materials were collected from an organic farm in Hong Kong. DNA of the samples were extracted and sequenced by metagenomic sequencing. The resistome of the samples was analysed using the resistome analysis pipeline ARGs-OAP v2.0. The abundance and the richness of the ARGs among the samples were compared using one-way ANOVA with Tukey post-hoc test. Results: COFFEE carried the highest copy number of ARGs per cell (2.771–3.539) and was significantly higher than that of CF (1.991–2.617) and GRASS (0.491–0.537). Multi-drug resistance genes predominated the resistome of COFFEE, for which the richness of the resistome was the lowest among the three materials (150–154 ARG subtypes). It was significantly lower than that of CF (203–229 ARG subtypes) but not that of GRASS (153–203 ARG subtypes). Conclusions: Contrary to the general belief that animal manure is the primary source of antibiotic resistance genes in organic composts, it was found that COFFEE carried the highest copy number of ARGs among the three materials, and multi-drug resistance genes predominated the resistome of COFFEE.