Analysis of the Concordance Between the Use of Phenotypic Screening Tests with the β-Lactamase Gene Profile in...

Background: There are many methods of identifying microbial resistance to therapeutic agents; however, they can generally be classified into two main categories: phenotypic and genotypic. The study aims to determine drug sensitivity and to analyze the correlation between the results obtained from cultures on commercial chromogenic media Brilliance^TM CRE (OXOID) and Brilliance^TM ESBL (OXOID) and the occurrence of specific resistance genes carbapenemase (IMP, NDM, VIM, KPC, OXA), ESBL β-lactamase (TEM, SHV, CTX-M), and AmpC (CMY, DHA), which will be used in drug sensitivity tests. Methods: The present study used bacteria, including Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli, obtained from patients hospitalized in military hospitals in Poland. All strains were plated on the commercial chromogenic media and subjected to antimicrobial susceptibility testing. Additionally, molecular assays detecting three main classes according to the mechanism of action, enzyme type carbapenemase (IMP, NDM, VIM, KPC, OXA), ESBL β-lactamase (TEM, SHV, CTX-M), and AmpC (CMY, DHA) were performed using the real-time PCR method. Results: The results of the studies indicate the presence of carbapenemases and ESBL genes. Among K. pneumoniae strains, the dominant gene was CTX-M-15 (88.89%), followed by the SHV (84.12%), NDM (46.03%), TEM (41.26%), KPC (34.92%), and OXA-48 (19.04%). In contrast, A. baumanii was dominated by carbapenemases from the OXA family (OXA-51 in 96.00% and OXA-24/40 in 84.00%). E. coli exhibits a high prevalence of CTX-M-15 (53.85%), TEM (46.15%), NDM (38.46%), and CMY-2 (30.77%). It was observed that the CTX-M-15 gene was commonly co-identified with SHV (n = 43). All tested strains grew on chromogenic Brilliance^TM CRE medium. In the case of Brilliance^TM ESBL medium, the genes determining the resistance mechanism were detected in 41.7% for A. baumannii, 53.8% for E. coli, and 100% for K. pneumoniae. Chromogenic media perfectly differentiate strains to species. A moderate positive correlation of the occurrence of the antibiotic resistance genes was observed for OXA-51 and OXA-24/40 genes, which were resistant to meropenem (rho = 0.45, p < 0.001). K-means cluster analysis performed on integrated genotype-phenotype data allowed for the identification of three distinct clusters characterized by distinct resistance gene profiles. These results demonstrate that selective agar media enable faster identification compared to other conventional techniques; however, the obtained results should be confirmed by other validated phenotypic methods, and, if possible, by a molecular assay.