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Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

Journal article
Authors Antti Karkman
K Pärnänen
D. G. Joakim Larsson
Published in Nature Communications
Volume 101
Issue 1
ISSN 2041-1723
Publication year 2019
Published at Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links https://doi.org/10.1038/s41467-018-...
Subject categories Bioinformatics (Computational Biology), Microbiology in the medical area

Abstract

Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.

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