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

Abstract

Objective: 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 the coronavirus disease 2019 (COVID-19) pandemic.

Methods: We conducted a multicenter, before-and-after, cross-sectional study to compare the rates of colonization and infection with CPE and/or CR-Ab in 2 study periods, period 1 (January-April 2019) and period 2 (January-April 2020). Incidence rate ratios (IRRs) and 95% confidence intervals (CIs) of weekly colonization and infection rates for each period were compared for the 2 study periods using Poisson regression. Weekly trends in the incidence of colonization or infection for each study period were summarized using local weighted (Loess) regression.

Results: We detected no significant change in either IRR and weekly trend in CPE colonization and infection during the 2 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 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 1 of the 3 centers, whereas they segregated in 2 different clusters in the other 2 centers, which strongly indicates horizontal transmission.

Conclusions: Our findings indicate the need to conduct infection control activities targeted against the spread of antimicrobial resistance between and within hospitals during the COVID-19 pandemic, and if necessary, remodulating them according to the new organizational structures imposed by the pandemic.

Fig. 1.

Weekly incidence of CR-Ab infection (a) and colonization (b); CPE-infection (c) and colonization (d). The incidence rate ration (IRR) was calculated only using data from week 6 through week 17 (blue shading between vertical dotted lines) corresponding to the activation of COVID units in 2020.

Fig 2.

Trends in ICU patient days from January through April in 2019 and 2020. Vertical dotted lines indicate the period with COVID units used to calculate the incidence rate ratio of infection.

Fig. 3.

Maximum likelihood phylogenetic tree based on the SNPs in the core genomes of Acinetobacter baumannii clinical strains included in this study.