Avian pathogenic Escherichia coli (APEC) is the most common cause of omphalitis. This disease affects newborn chicks up to the 7th day of life, causing high mortality and reduced performance of broilers. The study aimed to determine the frequency of APEC occurrence in embryos and newly hatched chicks. E. coli isolates were subjected to PCR to identify the minimal predictive virulence factors, phylogenetic groups, and predictive identification of the clonal complex (CC) ST131, ST117, and ST95. The phenotypic analysis assessed the antimicrobial resistance profile. A total of 254 samples were analyzed and 60.63% (n = 154/254) were positive for E. coli, of which 35.71% (n = 55/154) were classified as APEC (60% (n = 33/55) isolated in the yolk sac of day-old chicks, 29.09% (n = 16/55) in pipped eggs and 10.91% (n = 6/55) in embryonated eggs). The B2 phylogenetic group accounted for 21.81% (n = 12/55), with an increase in the contamination by B2 strains during the incubation process, from 6.25% (n = 1) to 30.30% (n = 10). We also identified 14.54% (n = 8/55) strains for the G group. The sequence types ST131 and ST117 were observed at the same frequency (10.90%, n = 6), followed by ST95 (3.6%, n = 2). A total of 27.27% were considered multidrug-resistant strains (MDR). The highest resistance rate was amoxicillin (43.64%, n = 24) and tetracycline (25.45%, n = 14). To a lesser extent, levels of resistance to critical drugs commonly used in hatcheries were identified, such as ceftiofur (20%, n = 11) and gentamicin (7%, n = 4).