Clinical Characteristics, Antibiotic Resistance Trends and Associated Molecular Epidemiology Traits in Escherichia coli Isolates Producing Neonatal Bacteremia

Abstract Background Escherichia coli is a leading cause of neonatal sepsis. This study’s objective was to investigate the clinical characteristics of newborns with E. coli bacteremia, and recent antibiotic resistance trends and molecular epidemiologic features of these invasive strains. Methods Clinical data and blood E. coli isolates collected from 54 neonates with bacteremia were studied. E. coli antibiotic susceptibility trends over time, and whole genome sequencing (WGS) data relevant to the genomic relatedness and capsule genotype of the isolates were analyzed. Results Thirty percent of bacteremic newborns were preterm. Mortality was 19% in preterm vs. 5% in term infants. Cerebrospinal fluid was collected in 43 (80%); meningitis was diagnosed in 28%. Necrotizing enterocolitis occurred in 2 neonates, both born preterm. Fifty-four percent of isolates were non-susceptible to ampicillin, and 7% to ceftriaxone. Non-susceptibility to cefazolin increased over time; rates for gentamicin and tobramycin were 11% for each antibiotic. WGS showed multiple sequence types (STs), of which ST95 (17%) was the most prevalent, followed by ST69 (11%), ST131 (7%), and ST12 (7%). K1 (43%) and K5 (20%) capsule genes were most prevalent. Conclusion Mortality due to E. coli sepsis remains high, especially in preterm newborns. Resistance to beta-lactams and aminoglycosides, the most common empiric treatments for E. coli sepsis, is worsening. Treatment regimens against neonatal E. coli sepsis need to be tailored according to evolving antibiotic resistance trends. Neonatal sepsis isolates are characterized by specific genomic traits indicative of virulent phenotypes that need continued surveillance.