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 re-appearance of organic farming. The interest of wide public in organic farming is affected by interest in animal welfare and lower use of antibiotics in organic than in conventional farming systems. On the other hand, the ambition to provide the animals with a more natural life 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 in fecal microbiota in slaughtered pigs kept under conventional and organic farming systems in Sweden, Denmark, France and Italy. Abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic resistance genes was determined by real time PCR genes in 468 samples and the faecal microbiota diversity was characterised in selected 48 samples by pyrosequencing of V3/V4 regions of 16S rRNA. Unlike expectation, there were no significant differences between the abundance of tested antibiotic resistance genes in microbiota of organic and conventional pigs within the same country. There were also no differences in 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 countries (Italy, France) exhibited significantly higher antibiotic resistance gene abundance than those from northern parts of Europe (Denmark, Sweden). Concerning the antibiotic resistance in fecal microbiota, the effect of geographic location of a herd therefore dominates over its organic or conventional production system status.One of the recent trends in animal production is the re-appearance of organic farming. The interest of wide public in organic farming is affected by interest in animal welfare and lower use of antibiotics in organic than in conventional farming systems. On the other hand, the ambition to provide the animals with a more natural life 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 in fecal microbiota in slaughtered pigs kept under conventional and organic farming systems in Sweden, Denmark, France and Italy. Abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic resistance genes was determined by real time PCR genes in 468 samples and the faecal microbiota diversity was characterised in selected 48 samples by pyrosequencing of V3/V4 regions of 16S rRNA. Unlike expectation, there were no significant differences between the abundance of tested antibiotic resistance genes in microbiota of organic and conventional pigs within the same country. There were also no differences in 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 countries (Italy, France) exhibited significantly higher antibiotic resistance gene abundance than those from northern parts of Europe (Denmark, Sweden). Concerning the antibiotic resistance in fecal microbiota, the effect of geographic location of a herd therefore dominates over its organic or conventional production system status.