Predicting Phenotypic Antimicrobial Resistance in Escherichia coli Isolates, Using Whole Genome Sequencing Data

Abstract

Background: The application of genotypic antimicrobial sensitivity tests (ASTs) is dependenton the reliability of the predictions of phenotypic resistance. In this study, routine AST resultsand the presence of corresponding antimicrobial resistance genes were compared. Methods: Eighty-four extended-spectrum-β-lactamase-producing Escherichia coli isolatesfrom poultry-related samples were included in the study. The disk diffusion method was usedto test for susceptibility to antimicrobial compounds, except colistin susceptibility, which wastested using the agar dilution method. Whole-genome sequencing (WGS) was performedusing a NextSeq 550 instrument (Illumina, USA). Antimicrobial resistance genes were detectedusing ResFinder 4.1. Results: Concordance rates between the genotype and phenotype ranged from 35.7%(ciprofloxacin) to 96.4% (tetracycline). The presence of tet was a good predictor of phenotypicresistance. Conclusion: The genotype was a good predictor of tetracycline phenotypic resistance, butthere was a gap in the prediction of phenotypic ASTs for trimethoprim-sulfamethoxazole,chloramphenicol, gentamicin, and ciprofloxacin. We concluded that WGS-based genotypicASTs are inadequate to replace routine phenotypic ASTs.