Genomic characteristics of clinical carbapenem-resistant Escherichia coli isolates in a tertiary hospital, 2013–2021

Background: Genomic characterization of carbapenem-resistant Escherichia coli (CREC) isolates is necessary to understand its transmission and implement infection control measures, given its potential threat to public health. Method: ： A total of 100 CREC isolates collected from 2013–2021 at a Nanjing tertiary hospital were analyzed using whole-genome sequencing (WGS). The distribution of resistant determinants (RTs), virulence factors (VFs), multi-locus sequence type (MLST), and FimH types was determined. Furthermore, a phylogenetic tree was constructed to investigate the genetic relationships. Result: All CREC strains (n=100) carried at least one carbapenem hydrolyzing ß-lactamase (CHßL)-encoding gene, with bla NDM (n=83, 83.0%) being the most common. Multiple RTs were detected with bla CTX (n=83, 83.0%) and bla TEM (n=78, 78.0%) being the most dominant ones. MLST identified 37 distinct STs, with ST167 (n=18, 18.0%) and ST410 (n=13, 13.0%) being the most predominant clones. Multiple plasmid replicons were found. The strains displayed 64 different virulence factors, with terC (n=98, 98.0%) and traT (n=76, 76.0%) being the most frequent. Genetic diversity was observed between the 100 CREC isolates, with clonal dissemination of ST167, ST361, ST2179, ST410, and ST131 being observed. Conclusion: The prevalence of bla NDM-5 , a major bla CHßLs , is concerning due to its distribution of various co-carried resistance genes and their potential to spread through multiple plasmid replicons. The isolates exhibit genetic diversity based on STs, Fim typing, serotyping, and phylogenetic tree analysis. ST167, ST361, ST2179, ST410, and ST131 are linked to clonal dissemination, highlighting the need for effective infection control measures to prevent their spread.