A standardized workflow for typing S. marcescens outbreaks using FT-IR spectroscopy.

Area of Science:

• Microbiology
• Spectroscopy
• Bioinformatics

Background:

• Serratia marcescens is an opportunistic pathogen frequently implicated in hospital-acquired infections.
• Accurate and rapid clonality assessment is crucial for effective infection control and outbreak management.
• Whole-genome sequencing (WGS) provides high-resolution data but can be time-consuming and expensive for routine screening.

Purpose of the Study:

• To evaluate the performance of Fourier-transform infrared (FT-IR) spectroscopy for clonality assessment of Serratia marcescens.
• To compare FT-IR spectroscopy's clustering output with whole-genome sequencing (WGS) using core genome single nucleotide polymorphism (cgSNP) analysis.
• To determine the utility of FT-IR spectroscopy as a rapid screening tool for clinical outbreaks.

Main Methods:

• Collected genetically diverse Serratia marcescens clinical isolates from Belgian hospitals.
• Measured isolates using FT-IR spectroscopy in biological triplicate for reproducibility.
• Utilized available WGS data for comparative performance assessment against FT-IR results.

Main Results:

• FT-IR spectroscopy demonstrated good concordance with WGS (Adjusted Rand Index [ARI] = 0.755).
• A single cut-off value (COV) was insufficient for reliable clinical outbreak interpretation.
• A standardized workflow with multiple COVs was developed and validated on three outbreak case studies, achieving clonality assessments within 24 hours.

Conclusions:

• FT-IR spectroscopy serves as an effective first-line screening tool for identifying clonal clusters of Serratia marcescens.
• This approach significantly reduces turnaround time for clonality assessment.
• Implementing FT-IR screening lowers the number of isolates requiring confirmatory WGS, decreasing overall outbreak investigation costs.