Epidemiology and Genetic Characteristics of Carbapenem-Resistant Escherichia coli in Chinese Intensive Care Unit Analyzed by Whole-Genome Sequencing: a Prospective Observational Study

This 4-month-long prospective observational study investigated the epidemiological characteristics, genetic composition, transmission pattern, and infection control of carbapenem-resistant Escherichia coli (CREC) colonization in patients at an intensive care unit (ICU) in China. Phenotypic confirmation testing was performed on nonduplicated isolates from patients and their environments. Whole-genome sequencing was performed for all E. coli isolates, followed by multilocus sequence typing (MLST), and antimicrobial resistance genes and single nucleotide polymorphisms (SNPs) were screened. The colonization rates of CREC were 7.29% from the patient specimens and 0.39% from the environmental specimens. Among the 214 E. coli isolates tested, 16 were carbapenem resistant, with the bla(NDM-5) gene identified as the dominant carbapenemase-encoding gene. Among the low-homology sporadic strains isolated in this study, the main sequence type (ST) of carbapenem-sensitive Escherichia coli (CSEC) was ST1193, whereas the majority of CREC isolates belonged to ST1656, followed by ST131. CREC isolates were more sensitive to disinfectants than were the carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates obtained in the same period, which may explain the lower separation rate. Therefore, effective interventions and active screening are beneficial to the prevention and control of CREC. IMPORTANCE CREC represents a public health threat worldwide, and its colonization precedes or occurs simultaneously with infection; once the colonization rate increases, the infection rate rises sharply. In our hospital, the colonization rate of CREC remained low, and almost all of the CREC isolates detected were ICU acquired. Contamination of the surrounding environment by CREC carrier patients shows a very limited spatiotemporal distribution. As the dominant ST of the CSEC isolates found, ST1193 CREC might be considered a strain of notable concern with potential to cause a future outbreak. ST1656 and ST131 also deserve attention, as they comprised the majority of the CREC isolates found, while bla(NDM-5) gene screening should play an important role in medication guidance as the main carbapenem resistance gene identified. The disinfectant chlorhexidine, which is used commonly in the hospital, is effective for CREC rather than CRKP, possibly explaining the lower positivity rate for CREC than for CRKP.