Investigation of antibiotic resistance genes in clinical Escherichia coli isolates and determination of the effect of some plant extracts on quinolon resistant isolates

Urinary tract infections (UTIs) are one of the most common bacterial infections affecting 150 million people worldwide each year, and the most common cause is uropathogenic Escherichia coli. In this study; the presence of β-lactamase encoding genes, virulence factor genes, class 1 integrons and plasmid-mediated quinolone resistance genes in 90 E. coli strains isolated from Turkey Rize Training and Research Hospital, Between November 2015-August 2016, were investigated by PCR. PCR result, integron positive samples were cloned into pGEM-T vector and sent to base sequence analysis. Results were evaluated using bioinformatics programs. The minimum inhibition concentrations (MIC) of the plant extracts of Mentha piperita L. (mint), Rosmarinus officinalis L. (rosemary), Curcuma longa (turmeric), Hypericum perforatum (yellow centaury), Camellia sinensis (green tea), Alkanna tinctoria (alkanet), Urtica dioica L. (nettle), Aloe vera L. (aloe vera), Tilia tomentosa (linden) were determined. The 90 E. coli isolates used in the study were identified by VITEK 2 Compact system. Antibiotic susceptibility test results showed that these isolates had low resistance rates for phosphomycin (2.7%), imipenem (3.2%) and meropenem (3.2%). However, resistance rates of ciprofloxacin (62.2%), trimethoprim sulfomethoxosol (75.6%) and ampicillin (61.1%) were found to be high. PCR results showed that 63% (57/90) of the strains carried class 1 integron gene cassettes and it was determined that class 1 integron carried dhfr gene cassette according to base sequence analysis. 52 strains (57%) carrying β-lactamase in CTX-M-2 group and 52 isolates carrying β-lactamase in CTX-M-1 group were detected. Plasmid-mediated quinolone resistance genes were also detected by PCR and the strains were found to carry 26% (24/90) qnrA, 6.6% (6/90) qnrB and 3.3% (3/90) qnrS genes. Eleven different virulence factor patterns were detected among 90 E. coli isolates. Fim (35 isolates) was identified as the most common virulence gene factor, while hly-fim, afa-aer-cnf-fim, aer-cnf, afa-aer and afa-cnf-fim patterns were observed in fewer strains. No virulence gene factor was detected in 14 of the isolates. The determination of MIC values of the plant extracts used in the study was performed by liquid microdilution method. The experiments were performed in three replications using 96 well-plates. As a result of the studies, Alkanna tinctoria extract showed the highest antibacterial activity and MIC values were found to be 1.25 mg / ml for EC58 and EC85 and MIC value of 2.5 mg / ml for EC50 and EC90.