The aim of the project is to develop methods and tools which can be used to get insight into the dynamics of acquired resistance genes (resistome) in the microbiome of piglets. Therefore, the diversity and the relative amounts among the various resistance genes present in tonsils, oro-nasopharynx and fecal samples obtained from piglets before and after treatment with antibiotics, will be determined.
The data obtained will then be correlated to the diversity observed among the microbiota detected in the same samples. In addition to these general resistome-microbiome studies we will focus on Escherichia coli and Staphylococcus aureus specifically. E. coli as well as S. aureus are of zoonotic organisms and resistant E. coli and S. aureus organisms can be a threat for human health. Moreover, in the current European and Dutch surveillance programs E. coli is used as an indicator organism to monitor diversity of antibiotic resistance genes as well as quantitative changes among the resistance genes in time and among samples. A comparison between general resistome-microbiome studies and E. coli and S. aureus specific studies will give insight into the predictive value of the use of E. coli and S. aureus as indicator organisms in surveillance programs.