Colibacillosis is a complicated disease causing severe economic losses and challenging veterinarians and producers. Therefore, this study aimed to characterize avian pathogenic Escherichia coli (APEC) strains causing respiratory troubles in chickens. Thirty broiler chicken flocks (2013-2016 outbreaks) at age of 17-35 days from Sharkia, Ismailia, Dakahlia and Sinai showed respiratory troubles and greenish diarrhea. The postmortem findings revealed typical colisepticemia picture including air sacculitis, fibrinous pericarditis and perihepatitis. The percentage of APEC isolation was 100 % while 10 flocks suffered mixed infections. From 284 collected samples (air sacs, heart blood, lungs and liver), E. coli isolation was mostly from air sacs (76.1 %) and lung (73.2 %) followed by heart blood (67.6%) and liver (54.9%). Based on serogrouping, the most common serogroups were O78 and O2 with percentage of 15% each. Based on antimicrobial disc diffusion test, the lowest (32.7 %) and highest resistance (100 %) were to doxycycline versus lincomycin, spiramycin, oxacillin and amoxicillin. PCR analysis for 55 MDR E. coli isolates revealed 3 antibiotic resistance genes (blaTEM (87.3 %), blaCTX-M (85.5 %) and blaOXA (5.5 %)) and 6 virulence genes in two multiplex PCR (iucD (96 %), Fim H (92.7 %), iss (76.4 %), ompT (58.2 %), tsh (45.5 %) and cvaC (9 %). An association between virulence and multidrug resistance genes in E. coli was concluded, that hindered the control strategy. Therefore, alternative strategies were necessary to minimize the antibiotic use and reduce the virulent strains occurrence.