Carbapenem-resistant bacteria in an intensive care unit during the coronavirus disease 2019 (COVID-19) pandemic: A multicenter before-and-after cross-sectional study

Objectives: To assess the incidence of colonization and infection with carbapenemase producing Enterobacteriaceae (CPE) and carbapenem resistant Acinetobacter baumannii (CR-Ab) in the ICUs of our city hospitals before and during COVID-19 pandemic. Methods: Multicentre before-after cross sectional study to compare the rates of colonization and infection with CPE and/or CR-Ab in two study periods, period 1 (Jan-Apr 2019) and period 2 (Jan-Apr 2020). Incidence rate ratios (IRR) and 95% CI of weekly colonization and infection rates for each period were compared for the two study periods with Poisson regression. Weekly trends in the incidence of colonization or infection for each study period were summarized using local weighted (Loess) regression. Results: There was no significant change in either IRR and weekly trend in CPE colonization and infection during the two study periods. A shift from KPC to other CPE mechanisms (OXA-48 and VIM) was observed during period 2. Compared to period 1, during period 2 the IRR of colonization and infection with CR-Ab increased of 7.5 and 5.5-fold, respectively. Genome sequencing showed that all CR-Ab strains belonged to the CC92/IC2 clonal lineage. Clinical strains clustered closely into a single monophyletic group in one of the three centres, whereas segregated in two different clusters in the other two centres, strongly appoints for the occurrence of horizontal transmission. Conclusion: Our findings remark the need of pursuing infection control activities targeted against the spread of antimicrobial resistance intra and inter hospitals during COVID-19 pandemic, and if necessary re-modulating them according to the new organizational structures imposed by the pandemic.