Leveraging whole-genome sequencing to manage a Streptococcus agalactiae outbreak in a neonatal intensive care unit

Abstract Objectives: To investigate late-onset Group B Streptococcus (GBS) transmission dynamics in a neonatal intensive care unit (NICU) using whole-genome sequencing (WGS). Setting: A 57-bed level III NICU in Toronto, Canada. Patients: Neonates with late-onset GBS (LOGBS) identified, July 2023–February 2024. Methods: An outbreak management team oversaw the investigation, hygiene audits, and stakeholder communications. Canada’s National Microbiology Laboratory performed WGS (Illumina) on outbreak and prior isolates. Core single nucleotide variant (SNV) phylogeny used SNVPhyl. Clinical data included age, infection type, maternal GBS status and outcome were reviewed. Three consecutive weekly point-prevalence surveys (PPS) were conducted using rectal and throat swabs. Results: In August 2023, two LOGBS cases (bacteremia and meningitis) triggered the investigation. Two more LOGBS bacteremias occurred pending WGS results. Three of the 4 isolates matched a prior early-onset (day-1) case (0 SNVs; cluster 1, serotype Ia). The fourth was 1 SNV different from a conjunctivitis case detected a week later (cluster 2, serotype V). PPS revealed 5 asymptomatic cases genomically unrelated to either cluster. In February 2024, two further LOGBS cases (bacteremia; asymptomatic bacteruria) emerged. The first matched the mother’s antepartum isolate with transmission to the second infant (0 SNVs; cluster 3, serotype IV). Hygiene audits identified gaps in hand and environmental safety; room proximity was the primary commonality. Following reinforcement of infection prevention measures, no further nosocomial GBS infections occurred through October 2025. Conclusions: This prolonged NICU outbreak involved multiple serotypes. WGS was critical in distinguishing horizontal transmission from independent introductions, directly guiding targeted infection control interventions.