Distinct Resistomes and Microbial Communities of Soils, Wastewater Treatment Plants and Households Suggest Development of Antibiotic Resistances Due to Distinct Environmental Conditions in Each Environment.

Laura Schages,Dirk Bockmühl,Florian Wichern,Stefan Geisen,Rainer Kalscheuer

doi:10.3390/antibiotics10050514

Abstract

The use of antibiotics in humans and animals results in a release of excess antibiotic residues into the environment through wastewaters and insufficient removal in wastewater treatment plants (WWTP), leading to increasing numbers of bacteria enriched in antibiotic resistance genes (ARG). However, the potential transfer of ARG and their host bacteria between different environments remains largely unexplored. Since many factors need to be fulfilled for a transfer between different environments, we hypothesized that antibiotic resistance (ABR) is less frequently transferred between environments in the same geographical region but rather develops and clusters in each distinct environment, leading to characteristic metagenome patterns in samples of different environments. We sampled agricultural soils, a WWTP and private households and performed metagenomic analyses to evaluate differences and potential overlaps in bacterial communities and resistomes of different environments. Wastewater revealed significantly higher richness of ARG (n = 40) and mobile genetic elements (n = 52) than soil and household samples. Bacterial communities differed between the environments and antibiotic resistance factors clustered distinctly. Overall, only few overlaps of ARG between the environments were observed, leading to the conclusion that ABR predominantly develops in individual environments as caused by environmental filtering for ARG, while a transfer between different environments is less likely.

Highlights

Antibiotic resistance (ABR) is prevalent even in the absence of anthropogenic impacts and prior to the therapeutic use of antibiotics [1,2], the number of antibioticresistant bacteria has increased rapidly with the use, overuse and misuse of antibiotics in human medicine and for veterinary purposes [3,4]
A transfer of antibiotic resistance (ABR) between the different environments is more limited to directly connected environments (e.g., HH to wastewater treatment plants (WWTP))
Despite its limitations, our study provides evidence that the transfer of antibiotic resistance genes (ARG) and antibioticresistant bacteria between different environments might be less important than focusing on the implementation of prevention measures in each individual environment

Summary

Introduction

Antibiotic resistance (ABR) is prevalent even in the absence of anthropogenic impacts and prior to the therapeutic use of antibiotics [1,2], the number of antibioticresistant bacteria has increased rapidly with the use, overuse and misuse of antibiotics in human medicine and for veterinary purposes [3,4]. Studies indicate that the resistome is mainly shaped by bacterial composition [12,13,14] and that similarities in taxonomic community composition lead to overlaps in mobile genetic element (MGE) and ARG prevalence [15] Analyzing both the resistome and bacterial community of different environments is crucial to identify potential reservoirs of ABR and possible transfer routes of antibiotic-resistant bacteria. It is not surprising that in many studies, metagenome analyses focusing on distinct sources such as wastewater, soil, surface water, humans and animals were performed [12,13,39,40], revealing the widespread occurrence of ABR In this field, households are virtually not studied and integrative crosshabitat studies to investigate potential transfer routes are rare

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