Genomic Insight into Escherichia coli Bloodstream Infections at a Tertiary Hospital in Shanghai: Predominance, Genetic Diversity, and Plasmid-Associated Virulence of CC131 and CC14

Background: Bloodstream infection (BSI) caused by Escherichia coli has become a growing clinical threat due to its high incidence and mortality rates. Despite its significant global health burden, the genomic diversity of E. coli in Shanghai has not been systematically investigated, with ramifications for treatment and prevention. This study aimed to assess the prevalence and genomic epidemiology of E. coli BSI isolates in Shanghai, delineate predominant lineages and their related phenotypic and genomic characteristics, and elucidate the population structure. Methods: A total of 136 E. coli strains were collected from a tertiary hospital in Shanghai between 2023 and 2024. We conducted comprehensive analyses, including multilocus sequence typing (MLST), core genome MLST (cgMLST), clonal complex assignment, serotype prediction, identification of antimicrobial resistance genes (ARGs) and plasmid-borne virulence genes, and plasmid mobility prediction. Results: The predominant clonal complex was CC131 (22.8%), followed by CC14 (14%). The highest resistance rate was observed for ampicillin (85.3%), whereas amikacin (3.7%), ertapenem (2.9%), imipenem (2.9%), minocycline (2.2%), and meropenem (2.2%) retained excellent in vitro activity. High resistance to ciprofloxacin (63.2%) and levofloxacin (62.5%) was observed, primarily mediated by mutations in gyrA (S83L, D87N) and parC (S80I), particularly in ST1193 strains. Plasmid-borne siderophore virulence genes co-occurred as gene modules, the majority of which were located on transferable IncFIB plasmids. However, this trend was not uniform across lineages, with the CC131 clones predominantly carrying mobilizable plasmids, while CC14 clones predominantly harbored non-mobilizable plasmids. Conclusions: Our findings reveal the dynamic genetic diversity of E. coli BSI isolates at a tertiary hospital in Shanghai, highlighting the importance of genomic surveillance and providing valuable insights for infection control.