Molecular Epidemiology of Carbapenem-Resistant P. aeruginosa and Enterobacterales Isolates from Clinical Infections and Their Susceptibility to Ceftazidime–Avibactam

The overuse of carbapenems has driven the rise of carbapenem-resistant <i>Pseudomonas aeruginosa</i> (CRPA) and <i>Enterobacterales</i> (CRE), against which ceftazidime-avibactam (CAZ-AVI) offers an alternative treatment. This study phenotypically determined resistance profiles of <i>P. aeruginosa</i> (PA), <i>Escherichia coli</i> (EC), and <i>Klebsiella pneumoniae</i> (KP) clinical isolates to CAZ-AVI and investigated molecular resistance mechanisms genotypically. A total of 394 PA, 90 EC, and 84 KP isolates were collected from the American University of Beirut Medical Center. Antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS) were performed on 30 isolates per species. Results showed that 100% of KP, 63% of EC, and 100% of PA isolates were carbapenem-resistant. Among these, 73% of KP, 79% of EC, and 60% of PA were CAZ-AVI-resistant. WGS revealed diverse sequence types, plasmids, and antimicrobial resistance genes. Additionally, 100% of KP, 93% of EC, and 89% of PA isolates produced metallo-β-lactamases (MBLs). Mutations in <i>ampD</i>, <i>ampR</i>, and <i>mexR</i> were identified in CAZ-AVI-resistant, non-MBL-producing PA, whereas mutations in <i>ompC</i>, <i>marR</i>, and <i>ampC</i> were detected in CAZ-AVI-resistant, non-MBL-producing EC. While CAZ-AVI remains effective against most CRE and CRPA lacking MBLs, resistance to CAZ-AVI is multifactorial, commonly involving overexpression of efflux pumps and AmpC β-lactamases, loss of porin channels, and the presence of oxacillinases.