A survey for phylogenetic relationship; presence of virulence genes and antibiotic resistance patterns of avian pathogenic and uropathogenic Escherichia coli isolated from poultry and humans in Yazd, Iran

Abstract Introduction Extra-intestinal infections in humans and poultry are caused by Extra-intestinal Pathogenic Escherichia coli strains (ExPEC) such as Avian Pathogenic E. coli (APEC) and Uropathogenic E. coli (UPEC). This study aimed to compare the presence of four pathogenic genes and antimicrobial resistance patterns of APEC and UPEC isolates, as well as investigating the phylogenetic relationship between these isolates by the Repetitive element sequence-based PCR (rep-PCR) method. Materials and methods 112 E. coli isolates were collected from poultry specimens in farms and 88 E. coli isolates from human urinary tract infection in the patients of the hospital in Yazd city during March 2015 to July 2016. Susceptibility testing was carried out using the disk diffusion method. PCR was performed to investigate the presence of fimH, iucC, sitA, and irp2 genes. Data were analyzed using SPSS software (version 16) and Chi-square test. Phylogenetic analysis was performed and analyzed by gel-comparison software for the rep-PCR method. Results The frequency of fimH, iucC, sitA, and irp2 genes was 67.8, 78.5, 84.8 and 89.2% for APEC and 96.5, 79.5, 86.3 and 75% for UPEC, respectively. Poultry strains exhibited multi-drug resistance to 16 antibiotics with the highest resistance to nalidixic acid and erythromycin, and all human isolates showed multi-drug resistance. The phylogenetic relationship was not found between human and poultry isolates by the rep-PCR method. Conclusion High antibiotic resistance was observed in isolates related to humans and poultry. Due to the presence of fimH, iucC, sitA, and irp2 genes in APEC and UPEC isolates, these genes are suggested to be effective in extra-intestinal E. coli infections. The phylogenetic relationship between the two pathotypes was not found by rep-PCR. Therefore, the hypothesis of transferring APEC to humans requires further investigation.