Investigation of phylogenetic characterization of poultry pathogeneic Eschericia coli isolates obtained from colibacillosis broiler before and after vaccination

Objective: To compare the changes in phylogenetic groups of avian pathogenic Escherichia coli (APEC) isolates obtained from broiler flocks vaccinated with commercial attenuated live E. coli vaccine, the effects of the vaccine on phylogenetic diversity, and the antibiotic resistance profiles of APEC isolates obtained at early and late stages of broiler life. Materials and Methods: The study material consisted of a total of 360 E. coli isolates, 180 before vaccination and 180 after vaccination, from 15 farms throughout 2022. Bacterial identification and antibiotic susceptibility tests were performed using the Gram-negative identification card (NMIC/ID-433) in the automated microbiology system (BD Phoenix 100™). Phylogenetic grouping of the isolates was performed using the Clermont multiplex PCR method targeting the chuA, yjaA, TspE4.C2 and arpA genes. The distribution of phylogenetic groups before and after vaccination was compared statistically using the chi-square (χ2) test. Results: Before vaccination, isolates were concentrated in groups B1 (22.8%), F (21.7%), E (21.1%), C (12.2%) and D (8.9%), respectively. After vaccination, groups A (56.7%) and B1 (27.2%) became dominant, while groups C, D and B2 were completely lost. While high resistance rates were detected against tetracycline and penicillin group antibiotics in the early stages of broiler life, a significant increase in resistance rates against tetracycline, penicillin, quinolone and folate group antibiotics was observed in the late stages. Conclusion: It was determined that commercial live attenuated E. coli vaccine applied to broilers caused remarkable changes in the distribution of phylogenetic groups, and had a significant effect especially on all phylogroups except phylogroup B1. This study showed that the isolates had high resistance rates to commonly used antibiotics, but low resistance levels were observed to clinically critical antibiotics such as colistin. Keywords: Drug resistance, Poultry, Vaccines, Escherichia coli, Phylogeny.