Using Metagenomic Approaches to Determine Antimicrobial Resistance Diversity and Prevalence within Four Landfills

Abstract

Antibiotics are one of the many hazardous substances present in municipal solid waste (MSW) landfills. Antibiotics can contaminate the leachate generated in landfills, which poses a threat to human health as leachate can permeate and contaminate the surrounding ground water and surface water systems. The presence of antibiotics in landfills can create selection pressures on the microorganisms present in the landfill, selecting for antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). This makes landfills important reservoirs of ARGs and ARB. This study used genome resolved metagenomic sequencing to observe ARG diversity and prevalence from four active municipal landfills, their adjacent ground or surface water systems, as well as other environments for comparison. The Resistance Gene Identifier (RGI) and DeepARG were used to predict resistance mechanisms, drug classes, and ARGs. The results from RGI and DeepARG highlighted landfill signatures that were distinct from other environments, and that landfill ARG profiles were more similar to each other than to other environments. PlasClass and Phage and Plasmid Recognizer for Metagenomes (PPR-Meta) were used to predict plasmids within the landfill metagenome datasets. Plasmids encoding ARGs were identified to assess the role of plasmids in ARG mobility in landfills, and to identify enriched ARG types on these mobile elements, such as multidrug resistance and antibiotic inactivation resistance mechanisms. The results of this study clarify target drug classes of interest, such as tetracyclines, aminoglycosides, macrolide-lincosamide-streptogramin (MLS) antibiotics, glycopeptides, and peptide antibiotics, as well as the impact that landfills along with their ground and surface water systems may have on surrounding environments.