Long-Term Temporal Stability of the Resistome in Sewage from Copenhagen

Abstract

ABSTRACT Antimicrobial resistance (AMR) is a major threat to global health, and it is crucial to understand the epidemiological aspects in order to predict the emergence and propagation of AMR genes. The aim of this study was to assess the variability and medium-term AMR trends within the mostly healthy human population of a single city. We monitored over 36 months (November 2015 to November 2018) the AMR level in the city of Copenhagen, Denmark, by taking bi-weekly sewage samples from the inlets of the three main water treatment plants, extracting the DNA, performing metagenomic sequencing, and read-mapping against a database of known AMR genes. We found that the AMR level was surprisingly stable with no periodic variability and no signs of drift over the measured period. We found, however, that the seemingly random variations at each site correlate in time with each other, suggesting that the variations we see are due to real environmental changes in the occurrence of AMR. IMPORTANCE The Copenhagen sewage resistome is surprisingly stable in time. The implication is that, at least for cities that are comparable to Copenhagen in terms of sewer infrastructure, few or even single samples provide a robust picture of the resistome within a city.

Keywords

• metagenomics
• antimicrobial resistance
• microbiome
• sewage