The study identified several chromosomal genes in Escherichia coli that affect antibiotic susceptibility, including acrA, acrB, tolC, crp, cyaA, hns, degP, pcnB, nikD, metL, and ompR. These genes were found to influence resistance to various antibiotics such as cefoxitin, norfloxacin, chloramphenicol, and minocycline.