Carbapenem-resistant Enterobacterales (CRE) are an urgent threat to healthcare, but the epidemiology of these antimicrobial-resistant organisms may be evolving in some settings since the COVID-19 pandemic. An updated analysis of hospital-acquired CRE (HA-CRE) incidence in community hospitals is needed.

We retrospectively analyzed data on HA-CRE cases and antimicrobial utilization (AU) from two community hospital networks, the Duke Infection Control Outreach Network (DICON) and the Duke Antimicrobial Stewardship Outreach Network (DASON) from January 2013 to June 2023. The zero-inflated negative binomial regression model was used owing to excess zeros.

126 HA-CRE cases from 36 hospitals were included in the longitudinal analysis. The pooled incidence of HA CRE was 0.69 per 100,000 patient days (95% confidence interval [95% CI], 0.57–0.82 HA-CRE rate significantly decreased over time before COVID-19 (rate ratio [RR], 0.94 [95% CI, 0.89–0.99]; p = 0.02), but there was a significant slope change indicating a trend increase in HA-CRE after COVID-19 (RR, 1.32 [95% CI, 1.06–1.66]; p = 0.01). In 21 hospitals participating in both DICON and DASON from January 2018 to June 2023, there was a correlation between HA-CRE rates and AU for CRE treatment (Spearman’s coefficient = 0.176; p < 0.01). Anti-CRE AU did not change over time, and there was no level or slope change after COVID.

The incidence of HA-CRE decreased before COVID-19 in a network of community hospitals in the southeastern United States, but this trend was disrupted by the COVID-19 pandemic.