Epidemiological Insights into Carbapenem-Resistant Enterobacterales Throughout the COVID-19 Pandemic in Buenos Aires, Argentina

Abstract

Background: Carbapenem-resistant Enterobacterales (CRE) are a global public health concern, with carbapenem-resistant Klebsiella pneumoniae (CR-Kp) recognised as the highestpriority pathogen. This study aimed to investigate the epidemiological features of CREisolates throughout the COVID-19 pandemic in Buenos Aires, Argentina. Methods: Aprospective study was conducted in two hospitals from 2019 to 2022, recovering all CREfrom inpatients. Antimicrobial susceptibility was performed by automated and/or manualtests, according to CLSI. β-lactamases detection was performed using Multiplex PCR andMALDI-TOF MS. Kp typing was assessed by multiplex PCR and/or MLST based on WGS.Results: 22% (359/1594) were CRE, predominantly CR-Kp. Overall, high non-susceptibility(NS) rates were observed in both centres. NS remained largely stable in HA, except for asignificant increase in colistin NS, whereas HB showed a rise in NS to multiple antimicrobials over time. A significant shift from multidrug-resistant to extensively drug-resistantand difficult-to-treat phenotypes was observed across the study periods. Out of 359 CRE,blaKPC was confirmed in 141, blaNDM in 170, and blaKPC + blaNDM in 20 isolates. Before theCOVID-19 pandemic, KPC was the main carbapenemase in HB, while NDM was alreadythe prevalent one in HA. In 2022, both enzymes showed similar prevalence. blaKPC-2 andblaNDM-5 were the prevalent alleles in K. pneumoniae. Before the COVID-19 pandemic,K. pneumoniae epidemiology varied by hospital, characterised by clonal diversity; however,in 2022, CG258-tonB79 drove the epidemiology in both hospitals. Conclusions: A moreextensive resistance phenotype among CRE was evidenced throughout the COVID-19pandemic, driven by carbapenemase-producing K. pneumoniae. NDM-5 and KPC-2 werethe main carbapenemases identified. A temporal shift in carbapenemase prevalence was observed in each hospital, converging in similar frequencies of KPC and NDM by 2022 acrossboth centres. This scenario was driven by the active dissemination of K. pneumoniae ST258.