title: Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments.
abstract: Antibiotics are commonly used in aquaculture and they can change the environmental resistome by increasing antibiotic resistance genes (ARGs). Sediment samples were collected from two fish farms located in the Northern Baltic Sea, Finland, and from a site outside the farms (control). The sediment resistome was assessed by using a highly parallel qPCR array containing 295 primer sets to detect ARGs, mobile genetic elements and the 16S rRNA gene. The fish farm resistomes were enriched in transposon and integron associated genes and in ARGs encoding resistance to antibiotics which had been used to treat fish at the farms. Aminoglycoside resistance genes were also enriched in the farm sediments despite the farms not having used aminoglycosides. In contrast, the total relative abundance values of ARGs were higher in the control sediment resistome and they were mainly genes encoding efflux pumps followed by beta-lactam resistance genes, which are found intrinsically in many bacteria. This suggests that there is a natural Baltic sediment resistome. The resistome associated with fish farms can be from native ARGs enriched by antibiotic use at the farms and/or from ARGs and mobile elements that have been introduced by fish farming.
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Windi I
authors.initials: WI
authors.lastname: Muziasari
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Katariina
authors.initials: K
authors.lastname: Pärnänen
authors.affiliation: Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, ON L8S 4L8, Canada Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA Food Safety and Enteric Pathogens Research Unit, USDA-ARS National Animal Disease Center, IA 50010, USA.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Johnson
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Christina
authors.initials: C
authors.lastname: Lyra
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Antti
authors.initials: A
authors.lastname: Karkman
authors.affiliation: Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Stedtfeld
authors.affiliation: Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland Department of Aquatic Ecology, Eawag, CH-8600 Dübendorf, Switzerland.
authors.forename: Manu
authors.initials: M
authors.lastname: Tamminen
authors.affiliation: Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland marko.virta@helsinki.fi.
authors.forename: Marko
authors.initials: M
authors.lastname: Virta
mesh_terms: D000617:Aminoglycosides / Q000494:pharmacology; D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D017756:Aquaculture / Q000379:methods*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005387:Finland; D005398:Fisheries; D005798:Genes, Bacterial; D019015:Geologic Sediments / Q000382:microbiology*; D032023:Integrons; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D008826:Microbial Sensitivity Tests; D009792:Oceans and Seas; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D018440:beta-Lactam Resistance / Q000235:genetics; D047090:beta-Lactams / Q000494:pharmacology
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S; D047090:beta-Lactams
keywords: Baltic Sea; environmental resistome; fish farms; mobile genetic elements; qPCR array; transposons