Enterobacterales gut colonization and late-onset sepsis in neonates: a multicentre prospective study across 18 neonatal intensive care units in six countries

Abstract

Objectives: Gram-negative bacteria cause a significant proportion of neonatal late-onset sepsis (LOS) and are associated with high mortality. Emerging evidence implicates the gut as a reservoir for invasive pathogens; however, the mechanisms of gut-to-blood translocation and the role of virulence factors remain unclear.

Methods: We conducted a secondary analysis of microbiological samples from the NeoMero-1 trial, a multicentre study of neonatal LOS. Whole-genome sequencing was performed on paired blood and faecal Enterobacterales isolates from 22 neonates with gram-negative bacteria bloodstream infection and concurrent gut samples. Genetic relatedness was assessed using multilocus sequence typing and species-specific single-nucleotide polymorphism thresholds. Virulence gene profiles were characterized using the virulence factor database.

Results: In 18 of 22 cases (82%), blood and gut isolates were genetically highly related, supporting gut-to-blood translocation. All invasive Escherichia coli (7 over 7) strains consistently harboured haemolysin genes (hlyA-D), absent in all the noninvasive strains (2/2 p 0.028). Extremely preterm and low birth weight neonates were overrepresented among those with translocation.

Conclusions: Our findings support the role of gut-derived Enterobacterales in the pathogenesis of neonatal LOS. These insights may inform infection control and targeted preventive strategies. Further prospective studies are needed to validate these findings and guide interventions for high-risk neonates.

Keywords: Gram negatives; Gut-blood; Neonatal sepsis; Virulome; Whole-genome sequencing.