Farm dust metagenomes in European poultry and pig farms

Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, Garcia-Cobos S, Dewulf J, Aarestrup FM, Wagenaar JA, Smit LAM, Mevius DJ, Heederik DJJ, Schmitt H; EFFORT-group. : : : : : [ Highlights ] -- An analysis of farm dust from 79 pig and poultry farms using metagenomics. -- Farm dust resistomes are compared to animal fecal and farmers stool resistomes. -- Farm dust bacterial microbiomes have an abundant and rich resistome. -- Animal fecal resistomes are an important, but not the only, source of farm dust ARGs. -- Antimicrobial usage in the animals is positively associated with dust resistome abundance. :: [ Objectives ] We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers stool resistomes was explored. [ Conclusion ] Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.
Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, Garcia-Cobos S, Dewulf J, Aarestrup FM, Wagenaar JA, Smit LAM, Mevius DJ, Heederik DJJ, Schmitt H; EFFORT-group. : : : : : [ Highlights ] -- An analysis of farm dust from 79 pig and poultry farms using metagenomics. -- Farm dust resistomes are compared to animal fecal and farmers stool resistomes. -- Farm dust bacterial microbiomes have an abundant and rich resistome. -- Animal fecal resistomes are an important, but not the only, source of farm dust ARGs. -- Antimicrobial usage in the animals is positively associated with dust resistome abundance. :: [ Objectives ] We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers stool resistomes was explored. [ Conclusion ] Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.