Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics
Journal article, 2016

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.

Risk assessment

Microbial ecology

Wastewater treatment

Antibiotic resistance genes


Fecal bacteria


Johan Bengtsson-Palme

University of Gothenburg

Rickard Hammarén

University of Gothenburg

C. Pal

University of Gothenburg

M. Ostman

Umeå University

Berndt Björlenius

Royal Institute of Technology (KTH)

Carl-Fredrik Flach

University of Gothenburg

Erik Kristiansson

Chalmers, Mathematical Sciences, Mathematical Statistics

University of Gothenburg

Jerker Fick

University of Gothenburg

M. Tysklind

Umeå University

D. G. Joakim Larsson

University of Gothenburg

Science of the Total Environment

0048-9697 (ISSN)

Vol. 572 697-712

Subject Categories

Infectious Medicine


Water Treatment





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