Asymptomatic human carriage of antimicrobially drug-resistant pathogens prior to infection is increasing worldwide. Further investigation into the role of this fecal reservoir is important for combatting the increasing antimicrobial resistance problems. Additionally, the damage on the intestinal microflora due to antimicrobial treatment is still not fully understood. Animal models are powerful tools to investigate bacterial colonization subsequent to antibiotic treatment. In this chapter we present a mouse-intestinal colonization model designed to investigate how antibiotics select for an ESBL-producing E. coli isolate. The model can be used to study how antibiotics with varying effect on the intestinal flora promote the establishment of the multidrug-resistant E. coli. Colonization is successfully investigated by sampling and culturing stool during the days following administration of antibiotics. Following culturing, a precise identification of the bacterial strain found in mice feces is applied to ensure that the isolate found is in fact identical to the strain used for inoculation. For this purpose random amplified of polymorphic DNA (RAPD) PCR specifically developed for E. coli is applied. This method allows us to distinguish E. coli with more than 99.95% genome similarity using a duplex PCR method.