Prospective whole genome sequencing to aid the identification and control of methicillin-susceptible Staphylococcus aureus transmissions in a neonatal ICU

Abstract

Background

Conventional surveillance methods may miss healthcare-associated pathogen transmission, particularly for common, drug-susceptible organisms. It is unclear if prospective genomic analyses can help identify otherwise silent transmission events and inform prevention efforts.

Methods

We sequenced methicillin-susceptible Staphylococcus aureus (MSSA) surveillance and clinical isolates in the neonatal intensive care unit (NICU) of an academic hospital between February 2022 and March 2024. Insights gleaned from genomic-epidemiologic analyses were used to control a large MSSA cluster and to calibrate infection control measures thereafter.

Findings

There were 2352 babies admitted during the 26-month study period, of whom 318 became colonized or infected with MSSA. Monthly MSSA incidence rates were largely stable throughout this period, but whole genome sequencing demonstrated 16 MSSA clusters (range 2–19 babies/cluster). Sequencing data integrated with epidemiologic analyses informed escalating infection control measures to control a sustained cluster of 19 babies infected with MSSA ST30 (including increased hand hygiene monitoring, enhanced environmental and equipment cleaning, contact precautions, decolonization of MSSA carriers), a subsequent decision against further intensification (foregoing screening all staff members for MSSA carriage), and the subsequent liberalization of some interventions (dropping contact precautions for lower risk babies). While intensified infection control measures controlled the primary ST30 cluster, low-level transmission events (range 2–8 babies) were detected throughout the study period despite those interventions.

Interpretations

Integrating prospective genomic and epidemiologic analyses of healthcare-associated pathogens can help identify unrecognized transmission clusters and inform and calibrate infection control response measures.

Summary

Prospective genotyping of surveillance and clinical methicillin-susceptible Staphylococcus aureus (MSSA) isolates in a neonatal intensive care unit over a 26-month period identified multiple MSSA clusters that were otherwise unappreciated and helped to both catalyze and calibrate infection control measures.