The spread of antibiotic resistance has limited the use of antibiotics in clinical settings, resulting in a huge threat to public health worldwide. Multidrug resistance causes thousands of deaths annually and is currently a significant financial burden in many countries. In this study, clinical isolates of Escherichia coli with varying drug resistance profiles were used to understand the genetic changes contributing to quinolone and β-lactam resistance. Novel genetic changes in gyrA and gyrB genes, known to contribute to quinolone resistance, were recorded. Furthermore, the CTX-M-14 and -15 genes were found in most β-lactam resistance strains. Significant correlations between mutations in novel genes and various phenotypic data were also observed, suggesting a role for these genes in determining these phenotypes. This work further increases our knowledge regarding causes of antibiotic resistance in clinical strains and lays foundation for future research.