Characterization of Carbapenem-Resistant Escherichia coli Isolates Through the Whole-Genome Sequencing Analysis

Limited studies have characterized multiple carbapenem-resistant Escherichia coli isolates and compared their genetic characteristics through whole-genome sequencing (WGS) because of the scarcity of these isolates. In this study, we determined the prevalence of carbapenem resistance in 2,993 E. coli isolates collected from three Chinese hospitals. The carbapenem-resistant isolates were further characterized by WGS, and the molecular epidemiological characters and resistance mechanisms were explored through the publicly available platforms from the Center for Genomic Epidemiology. Twenty-four carbapenem-resistant E. coli isolates were screened out from 2,993 E. coli clinical isolates and all carbapenem-resistant isolates showed multiple drug-resistant phenotypes. The main serotypes identified among carbapenem-resistant isolates through WGS included E. coli O8:H21 (n = 6), E. coli O102:H6 (n = 6), and E. coli O25:H4 (n = 3), and the dominant sequence types (ST) were ST410 (n = 8), ST405 (n = 6), and ST131 (n = 3). Carbapenemase encoding genes, including bla_IMP-4 (n = 3), bla_KPC-2 (n = 2), bla_NDM-5 (n = 1), and bla_IMP-1 (n = 1) were identified in seven isolates. WGS analysis could provide a vast amount of molecular epidemiological data of the resistant isolates all at once, such as serotypes, multilocus sequence typing (MLST) types, plasmid replicons, and resistant determinants. Since carbapenem is the last resort to treat life-threatening E. coli infections, it is urgent to characterize the transmission routes and develop risk management strategies to block or slow down the transmission of resistance mechanisms and save carbapenems.