Cluster of carbapenemase-producing enterobacterales secondary infections during the COVID-19 crisis at a New York City Hospital

Background: Patients with COVID-19 may be at increased risk for secondary bacterial infections At our quaternary care hospital in New York City, the rapid escalation of COVID-19 cases was accompanied by a massive surge in the need for hospital and critical care capacity During this time, we noted a increase in infections caused by carbapenemase-producing Enterobacterales (CPE) Methods: We retrospectively assessed microbiology data to identify patients with positive testing for SARS-CoV-2 who had clinical cultures with meropenem-resistant and/or carbapenemase gene-positive Enterobacterales We obtained microbiological and clinical data by manual chart review Available clinical isolates underwent long-range genomic sequencing using the MinION (Oxford) for rapid genotyping, resistance gene detection, and phylogenetic analysis Results: From March 1 to May 18, we identified 33 CPE isolates from 13 patients, including 29 Klebsiella pneumonia and four Enterobacter cloacae Most patients (11/13) had a positive respiratory culture, and 7/13 developed bacteremia All patients had prolonged, complex hospitalizations with extensive antibiotic exposure We performed long-range sequencing on 19 isolates from 12 patients 15/16 K pneumoniae isolates belonged to sequence type (ST) 258 encoding KPC (14 KPC-2;1 KPC-3);one ST70 isolate encoded KPC-2 All four E cloacae isolates belonged to ST270 and encoded NDM-1 Phylogenetic analysis of ST258 isolates including historical isolates from our hospital revealed a distinct lineage of isolates from COVID-19 patients (72% bootstrap support), with expected clustering of isolates from the same patient and patients that were cohorted together Conclusion: While CPE have declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a reemergence of these highly resistant pathogens in the wake of the global pandemic System-level factors, such as the rapid scale-up of critical care capacity, while clearly needed to address the unprecedented reach of COVID-19, may have contributed to isolate clustering in these patients Increased surveillance and antimicrobial stewardship efforts will be needed to mitigate the impact of CPE in the future