Antimicrobial resistance in the farm environment: determinants of the resistome of animal feces and airborne dust

Antimicrobial resistance (AMR) is a growing global health problem for humans and animals. Livestock can be a reservoir of resistant bacteria and resistance genes (the pieces of DNA that code for resistance in bacteria), which are excreted with feces and then spread around the farms and enter the surrounding environment. In this thesis the detection of antimicrobial resistance in animal manure was performed with shotgun metagenomics. With this sequencing technique we were able to examine all known resistance genes and bacteria present in our samples. It showed us that fecal samples of pigs and poultry include hundreds of different resistance genes with higher concentrations in pig feces than in poultry feces. Although antibiotic use in animals was a relevant determinant, it explained the presence of resistance genes in animal feces only partially. A route of transmission within and around livestock farms is via air. Small particles of, inter alia, manure, which contain resistant bacteria aerosolize and can subsequently spread into the environment. Indeed we showed that the presence of resistance genes in animal manure is correlated with resistance genes in airborne dust from the same stables, however dust seems to harbor more resistance genes than those found in feces from livestock. Other relevant drivers for the composition and concentration of resistance genes in airborne farm dust are the bacteria present in dust, the season and biosecurity measures on the farm. This thesis will help to understand the complex problem of AMR in livestock farms and hopefully encourage researchers and policymakers to include the farm and animal environment in their future work