Uncovering the Resistance Mechanisms in Extended-Drug-Resistant Clinical Isolates: Insights from Gene Expression and Phenotypic Tests.

(1) Background: The purpose of the study was to describe the activity of efflux pumps in Multidrug-Resistant (MDR) clinical isolates of and to compare the carbapenem-resistance identification tests with PCR; (2) Methods: Sixty MDR were analyzed for detection of carbapenemase by disk diffusion inhibitory method, carbapenem inactivation method and Modified Hodge Test. Endpoint PCR was used to detect 7 carbapenemase genes (, , , , , , ) and for colistin resistance. The expression of A, B, C, E and X genes corresponding to the four main efflux pumps was also evaluated; (3) Results: From the tested strains, 71.66% presented at least one carbapenemase gene, with as the most occurring gene (63.3%). Compared with the PCR, the accuracy of phenotypic tests did not exceed 25% for . The efflux pump genes were present in all strains except one. In 85% of the isolates, an overactivity of A, B and mostly C was detected. Previous treatment with ceftriaxone increased the activity of C by more than 160 times; (4) Conclusions: In our MDR clinical isolates, the carbapenem resistance is not accurately detected by phenotypic tests, due to the overexpression of efflux pumps and in a lesser amount, due to carbapenemase production.