Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal...

Area of Science:

• Infectious Diseases
• Genomics
• Epidemiology

Background:

• An increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections was observed in a Dutch neonatal intensive care unit.
• Traditional methods like spa typing and Multiple-Locus Variable number tandem Repeat Analysis (MLVA) were used for outbreak tracing but had limitations.

Purpose of the Study:

• To investigate the utility of whole-genome sequencing (WGS) for enhanced MSSA outbreak tracing in a neonatal intensive care unit.
• To compare WGS with traditional typing methods for accuracy and resolution in identifying transmission routes.

Main Methods:

• Whole-genome sequencing (WGS) was performed on MSSA isolates from neonatal infections, carriage surveillance, and healthcare workers (HCWs).
• Bioinformatic analysis identified single nucleotide polymorphisms (SNPs) to assess genetic relatedness.
• The genetic diversity of the background surveillance population was measured to define transmission-level relatedness.

Main Results:

• WGS provided higher resolution and accuracy in genomic outbreak analyses compared to spa typing and MLVA.
• MLVA incorrectly clustered some isolates, while WGS provided a more accurate picture of transmission.
• HCWs were implicated in multiple outbreaks, but WGS also alleviated concerns regarding a specific HCW.

Conclusions:

• WGS, particularly when including the circulating background population, significantly improves genomic outbreak inference in healthcare settings.
• The enhanced resolution and accuracy of WGS enable more effective control measures for nosocomial infections.
• Incorporating WGS into routine surveillance can overcome limitations of traditional typing methods for pathogen transmission studies.