Gut Colonization With Carbapenem-Resistant Enterobacteriaceae in COVID-19-Recovered Patients: A Prospective Observational Study.

Background The COVID-19 pandemic was associated with widespread empirical antibiotic use, raising concerns regarding disruption of gut microbiota and emergence of antimicrobial resistance. We evaluated intestinal colonization with carbapenem-resistant Enterobacteriaceae (CRE) among COVID-19-recovered patients and compared them with non-COVID controls. Methods In this prospective observational study conducted at a tertiary care center between December 2021 and March 2023, stool samples were collected from COVID-19-recovered patients who required hospitalization, COVID-19-negative controls from the community, and hospitalized COVID-19-negative controls. Samples were cultured for CRE. CRE isolates were cultured on selective media and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subsequently underwent molecular characterization for carbapenem resistance genes using the Xpert® Carba-R assay. Results A total of 266 participants were enrolled, comprising 87 COVID-19-recovered patients, 77 community controls, and 102 COVID-19-negative hospitalized controls. Within the COVID-19-recovered group, 20 patients (23%) had mild disease, 33 (38%) moderate, and 34 (39%) severe disease. CRE colonization was identified in 54 of 87 (62%) COVID-19-recovered patients, 50 of 77 (65%) community controls, and 56 of 102 (55%) hospitalized controls. NDM-1 and OXA-48 were the predominant carbapenemase genes detected among the CRE isolates. Conclusions Gut colonization with CRE was highly prevalent across all study groups. Hospitalization for COVID-19 was not associated with a higher prevalence of colonization compared with controls. Continued antimicrobial resistance surveillance and antibiotic stewardship remain essential in the post-pandemic era.