Antimicrobial resistance patterns and phylogenetic analysis of Shiga toxin-producing Escherichia coli strains from goats using both Clermont phylogenetic schemes

Abstract

Foodborne transmission of Shiga toxin-producing Escherichia coli (STEC) poses a threat to public health. The Clermont typing schemes (previous and revised) have been used widely to phylotype E. coli. The present study was conducted to compare the relationship of the Clermont phylogenet-ic schemes in STEC strains isolated from goats and antibiotic resistance patterns in the southeast of Iran. Overall 52 strains carrying the stx gene were used for subsequent analysis. All strains were determined by analysing the genomic DNA with a PCR-based method using the two Clermont et al. (2000, 2013) schemes. Extended spectrum beta-lactamase (ESBL) producing strains were con-firmed by the double disk-diffusion method. STEC strains were also tested for susceptibility to 20 antimicrobials agents. In the original Clermont method, the prevalent phylogroups were B1 (69.2%) and A (28.8%). The significant phylogenetic groups of strains according to the revised Clermont method were B1 (82.7%), A (13.5%) and unknown (3.8%). However, STEC strains underwent changes as noted from A to B1 (17.3%), B1 to unknown (3.8%), B1 to A (1.9%) and D to B1 (1.9%) groupings. Of the 52 stx-positive strains, two ESBL producing strains were detected. Susceptibility data showed that the most frequent resistance phenotype was related to cefazolin (90.4%), streptomycin (88.5%), ampicillin (86.5%) and oxytetracycline (82.7%) respectively. Alt-hough the overall frequency of the reassigned phylotypes was not significant, most changes oc-curred within the A phylotype. Therefore, implementation of the new method on isolates belong-ing to the A phylotype in the old method seems to be necessary to obtain accurate results.