Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients

BackgroundColonization with multidrug resistant E. coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients, and to identify evolutionary changes and strain replacement events within patients. MethodsPatients were admitted to the intensive care unit and haematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. ResultsThe E. coli isolates were genetically diverse, with 13 sequence types (STs) identified among 21 isolates sequenced. Five patients were colonized by ST131 encoding CTX-M-27, a type of beta-lactamase gene not previously been observed in Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. ConclusionOur study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131 encoding CTX-M-27, which appears to be emerging as a globally important multidrug resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.