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Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Journal article
Authors Johan Bengtsson-Palme
Rickard Hammarén
Chandan Pal
Marcus Östman
Berndt Björlenius
Carl-Fredrik Flach
Jerker Fick
Erik Kristiansson
Mats Tysklind
D. G. Joakim Larsson
Published in Science of the Total Environment
Volume 572
Pages 697-712
ISSN 0048-9697
Publication year 2016
Published at Department of Mathematical Sciences, Mathematical Statistics
Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Pages 697-712
Language en
Links dx.doi.org/10.1016/j.scitotenv.2016...
Keywords Antibiotic resistance genes, Co-selection, Fecal bacteria, Microbial ecology, Risk assessment, Wastewater treatment
Subject categories Infectious Medicine, Water Treatment, Microbiology

Abstract

Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.

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