Aim To assess the effect of antibiotics administered in feed on the resistance phenotypes and genotypes of Escherichia coli in the chicken intestine. Method and Results Chickens were administered amoxicillin, chlortetracycline and florfenicol in feed and 203 intestinal E. coli were examined for their susceptibility to 11 antimicrobial agents and for the presence of antibiotic resistance genes (ARG) using PCR. DNA was extracted from chicken stool samples in 15, 20, 30 and 40 day old chickens. We found that while antibiotic resistance rates increased with time, the relative gene abundance of tet(W), tet(A), cmlA, cfr and sul1 decreased. In contrast, the relative abundance of gene bla(TEM) and mcr-1 increased over the experimental period. Pearson correlation analysis indicated that sul1 was correlated with tet(W) (R = 0 center dot 630, P < 0 center dot 01) and cmlA was correlated with cfr (R = 0 center dot 587, P < 0 center dot 01). Interestingly, mcr-1 correlated with tet(W) (R = -0 center dot 546, P < 0 center dot 05). Conclusions Administration of different antibiotic reduced the relative abundance of ARG in chickens but did not halt the expansion of antibiotic resistance. Significance and Impact of the Study Changing the pattern of antibiotic types used to prevent antibiotic resistance in chickens is not a viable method to prevent the spread of ARG.