Early-Onset Infection Caused by Escherichia coli Sequence Type 1193 in Late Preterm and Full-Term Neonates

Emerg Infect Dis. 2024 Jan;30(1):20-28. doi: 10.3201/eid3001.230851.


Using whole-genome sequencing, we characterized Escherichia coli strains causing early-onset sepsis (EOS) in 32 neonatal cases from a 2019-2021 prospective multicenter study in France and compared them to E. coli strains collected from vaginal swab specimens from women in third-trimester gestation. We observed no major differences in phylogenetic groups or virulence profiles between the 2 collections. However, sequence type (ST) analysis showed the presence of 6/32 (19%) ST1193 strains causing EOS, the same frequency as in the highly virulent clonal group ST95. Three ST1193 strains caused meningitis, and 3 harbored extended-spectrum β-lactamase. No ST1193 strains were isolated from vaginal swab specimens. Emerging ST1193 appears to be highly prevalent, virulent, and antimicrobial resistant in neonates. However, the physiopathology of EOS caused by ST1193 has not yet been elucidated. Clinicians should be aware of the possible presence of E. coli ST1193 in prenatal and neonatal contexts and provide appropriate monitoring and treatment.

Keywords: Escherichia coli; France; ST1193; ST95; antimicrobial resistance; bacteria; meningitis/encephalitis; molecular epidemiology; neonatal sepsis; sequence type; virulence; whole-genome sequencing.

Publication types

  • Multicenter Study

MeSH terms

  • Anti-Bacterial Agents / therapeutic use
  • Escherichia coli
  • Escherichia coli Infections* / drug therapy
  • Escherichia coli Infections* / epidemiology
  • Female
  • Humans
  • Infant, Newborn
  • Phylogeny
  • Pregnancy
  • Prospective Studies
  • Sepsis* / drug therapy
  • Virulence


  • Anti-Bacterial Agents