Abstract

Background: Carbapenem-resistant Enterobacterales (CRE) are a major public health threat, largely due to the presence of carbapenemases, which are globally disseminated in mobile genetic elements. The emergence of CRE carrying multiple carbapenemases has been reported in several countries, particularly after the COVID-19 pandemic. In this study, we report the emergence of dual-producing CRE (DP-CRE) in Chile and provide a phenotypic and genomic characterization using whole-genome sequencing (WGS). Methods: We evaluated the presence of carbapenemases in a total of 1367 CRE isolates recovered from invasive infections in 11 healthcare centers since 2018. Among them, 9 DP-CRE were detected and included in this report. Antimicrobial susceptibility was tested by broth microdilution and disk diffusion methods (CLSI 2023), while blaKPC, blaVIM, blaIMP and blaNDM genes were detected by PCR. WGS was carried out using short and long reads (Illumina and Oxford Nanopore) and hybrid assemblies were performed. Results: All 9 DP-CRE identified were recovered between November 2021 and June 2022 from 3 healthcare centers of a single city. In terms of species, 6 were identified as E. coli, one isolate of K. pneumoniae, one K. oxytoca and one C. freundii. All DP-CRE identified carried the combination of blaKPC and blaNDM. Genomic analyses confirmed all but one isolate carried blaKPC-2 and blaNDM-7. The remaining genome belonged to a K. pneumoniae that harbored blaKPC-3 and blaNDM-7. All 9 isolates exhibited resistance to all beta-lactams, including carbapenems, aztreonam (ATM), cephalosporins and beta-lactam/beta-lactamase inhibitors. Cefiderocol (FDC) was the only compound active against all the isolates. Also, all DP-CRE isolates became susceptible to ATM when combined with ceftazidime/avibactam (CZA). Hybrid assemblies revealed that blaKPC and blaNDM were harbored on independent plasmids (~58,900 bp and ~41,100 bp, respectively). Conclusions: To the best of our knowledge, this is the first report of the emergence of DP-CRE in Chile in COVID-19 pandemic. Our results highlight the relevance of active surveillance of multidrug-resistant pathogens. FDC and CZA/ATM were the only compounds that remained active in vitro against these pathogens.