title: Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.
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.
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Bengtsson-Palme
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden.
authors.forename: Rickard
authors.initials: R
authors.lastname: Hammarén
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.
authors.forename: Chandan
authors.initials: C
authors.lastname: Pal
authors.affiliation: Department of Chemistry, Umeå University, Umeå, Sweden.
authors.forename: Marcus
authors.initials: M
authors.lastname: Östman
authors.affiliation: Division of Industrial Biotechnology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Berndt
authors.initials: B
authors.lastname: Björlenius
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.
authors.forename: Carl-Fredrik
authors.initials: CF
authors.lastname: Flach
authors.affiliation: Department of Chemistry, Umeå University, Umeå, Sweden.
authors.forename: Jerker
authors.initials: J
authors.lastname: Fick
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Kristiansson
authors.affiliation: Department of Chemistry, Umeå University, Umeå, Sweden.
authors.forename: Mats
authors.initials: M
authors.lastname: Tysklind
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden. Electronic address: joakim.larsson@fysiologi.gu.se.
authors.forename: D G Joakim
authors.initials: DGJ
authors.lastname: Larsson
mesh_terms: D000900:Anti-Bacterial Agents / Q000032:analysis; D001419:Bacteria / Q000187:drug effects / Q000235:genetics; D004251:DNA Transposable Elements; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics; D004352:Drug Resistance, Microbial / Q000187:drug effects / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D008670:Metals / Q000032:analysis; D012336:RNA, Ribosomal, 16S; D012641:Selection, Genetic; D012722:Sewage / Q000382:microbiology*; D013548:Sweden; D014865:Waste Disposal, Fluid / Q000379:methods*; D014874:Water Pollutants, Chemical / Q000032:analysis
chemical_list: D000900:Anti-Bacterial Agents; D004251:DNA Transposable Elements; D008670:Metals; D012336:RNA, Ribosomal, 16S; D012722:Sewage; D014874:Water Pollutants, Chemical
keywords: Antibiotic resistance genes; Co-selection; Fecal bacteria; Microbial ecology; Risk assessment; Wastewater treatment