Self-controlled Cohort Study of the Amplification and Selection of Antimicrobial Resistance in the Human Intestine

The worldwide increase in the incidence of multidrug-resistant (MDR) pathogens is alarming. Antimicrobial treatment is a risk factor for the isolation of MDR pathogens and can therefore contribute to the observed trend. Differences in the degree of selection pressure caused by various antimicrobials have not been systematically investigated until today. The aim of the proposed project is the determination of the impact of antibiotic treatment on the copy number of resistance genes in the human intestinal microbiome using metagenome shotgun sequencing. The resistance gene count in the gastrointestinal tract will be determined in a clinical cohorts of patients treated with either ciprofloxacin or cotrimoxazol as monotherapy. The subsequent quantification and comparison of the selection pressure facilitates the application of antibiotics with a lower potential to select for resistance. To achieve this goal, a self-controlled, prospective observational epidemiological study will be performed at two centres of the German Centre for Infection Research (Tübingen, Cologne).