title: Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries.
abstract: One of the recent trends in animal production is the revival of interest in organic farming. The increased consumer interest in organic animal farming is mainly due to concerns about animal welfare and the use of antibiotics in conventional farming. On the other hand, providing animals with a more natural lifestyle implies their increased exposure to environmental sources of different microorganisms including pathogens. To address these concerns, we determined the abundance of antibiotic resistance and diversity within fecal microbiota in pigs kept under conventional and organic farming systems in Sweden, Denmark, France and Italy. The abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic resistance genes was determined in 468 samples by real-time PCR and the fecal microbiota diversity was characterized in 48 selected samples by pyrosequencing of V3/V4 regions of 16S rRNA. Contrary to our expectations, there were no extensive differences between the abundance of tested antibiotic resistance genes in microbiota originating from organic or conventionally housed pigs within individual countries. There were also no differences in the microbiota composition of organic and conventional pigs. The only significant difference was the difference in the abundance of antibiotic resistance genes in the samples from different countries. Fecal microbiota in the samples originating from southern European countries (Italy, France) exhibited significantly higher antibiotic resistance gene abundance than those from northern parts of Europe (Denmark, Sweden). Therefore, the geographical location of the herd influenced the antibiotic resistance in the fecal microbiota more than farm's status as organic or conventional.
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Lenka
authors.initials: L
authors.lastname: Gerzova
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Babak
authors.affiliation: Brno University of Technology, Brno, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Sedlar
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Marcela
authors.initials: M
authors.lastname: Faldynova
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Videnska
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Darina
authors.initials: D
authors.lastname: Cejkova
authors.affiliation: Technical University of Denmark, National Food Institute, Copenhagen, Denmark.
authors.forename: Annette Nygaard
authors.initials: AN
authors.lastname: Jensen
authors.affiliation: Anses, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Denis
authors.affiliation: Anses, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France.
authors.forename: Annaelle
authors.initials: A
authors.lastname: Kerouanton
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy.
authors.forename: Antonia
authors.initials: A
authors.lastname: Ricci
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: Cibin
authors.affiliation: National Veterinary Institute (SVA), Uppsala, Sweden.
authors.forename: Julia
authors.initials: J
authors.lastname: Österberg
authors.affiliation: Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Ivan
authors.initials: I
authors.lastname: Rychlik
mesh_terms: D000822:Animal Husbandry; D000818:Animals; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005062:European Union; D005243:Feces / Q000382:microbiology*; D005798:Genes, Bacterial / Q000235:genetics; D064307:Microbiota / Q000235:genetics*; D058871:Organic Agriculture; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013552:Swine / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S