Molecular Characterization of a Rare ESBL E. coli Strain Causing a Necrotizing Enterocolitis Outbreak in Preterm Infants.

Background: Necrotizing enterocolitis (NEC), a severe comorbidity of prematurity, is usually sporadic, but occasional outbreaks suggest an infectious cause. Escherichia coli , the most frequent Gram-negative pathogen in preterm infants, historically displays a low inhospital transmissibility.

Aim: To report the management of an NEC outbreak in a Belgian neonatal intensive care unit and the molecular characterization of a rare, highly virulent/resistant E. coli strain.

Methods: Clinical data were extracted from electronic medical records. Surveillance and clinical isolates characterized using standard methods were secondarily analyzed by bacterial whole-genome sequencing using EnteroBase for phylogenic classification and BioNumerics for resistance and virulence profile determination.

Findings: A cluster of 6 infants was colonized by a single extended-spectrum beta-lactamase-producing E. coli strain in a 1-month period. Four infants developed severe NEC, resulting in 1 death and 3 short bowel syndromes. Although the index infant and his twin sibling acquired the strain vertically from their mother, transmission occurred horizontally through caregivers in subsequent cases. Enhanced infection prevention and control measures allowed containment of the outbreak. Molecular typing of the strain revealed a single, previously unregistered O6:H1 serotype of extraintestinal pathogenic E. coli , urinary pathogenic E. coli harboring multiple resistance and virulence genes, including extended-spectrum beta-lactamase-encoding blaCTX-M-15 and fimbriae-encoding papA .

Conclusion: The emergence of high-virulence strains in neonatal intensive care units calls for the implementation of enhanced infection prevention and control strategies. Bacterial genomic sequencing techniques, if implemented in multidrug-resistant organism screening, could represent a valuable addition for early characterization of virulence and resistance profiles, and improve prevention and containment of infectious outbreaks.