Comparisons were made of the performance of different regression models for analysis of annual variation in susceptibility of generic Escherichia coli isolates to ceftiofur, ampicillin and nalidixic acid from retail chicken surveillance. Secondly, impacts of using different multidrug resistance (MDR) classification metrics for the analysis of annual variation in MDR were evaluated using generic E.coli isolates from chicken abattoir surveillance. Antimicrobial susceptibility data were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance. Model assumptions were met using logistic and multinomial regression. Linear, tobit, ordinal and complementary log-log regression did not meet model assumptions and/or did not perform well. Significant annual variation in susceptibility to all three antimicrobials was identified with multinomial regression, whereas logistic regression only identified significant annual variation in susceptibility to ceftiofur. Both the prevalence of MDR and interpretation of the association between MDR, and year and region differed depending on the MDR classification metric used.