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

PURPOSE: In this study, we evaluated the performance of FT-IR spectroscopy for clonality assessment of Serratia marcescens by comparing its clustering output to that of whole-genome sequencing (WGS), using core genome single nucleotide polymorphism (cgSNP) analysis as reference. METHODS: A genetically diverse set of Serratia marcescens clinical isolates was collected from different hospitals in Belgium and measured with FT-IR spectroscopy in biological triplicate to assess reproducibility and in turn build a robust reference set. WGS data of the isolates was available and used to assess the performance of FT-IR spectroscopy. RESULTS: FT-IR spectroscopy showed good overall concordance with WGS (Adjusted Rand Index [ARI] of 0.755), but the level of agreement was insufficient to support the use of a single fixed cut-off value (COV) for clinical outbreak interpretation. To address this, a standardized workflow was developed incorporating multiple COVs to interpret clustering with varying level of confidence. This approach was validated using three unrelated S. marcescens outbreak case studies in neonatal intensive care units. The workflow yielded clustering results that matched WGS-based analyses and allowed clonality assessments within 24 h after isolate recovery. CONCLUSION: In conclusion, FT-IR spectroscopy can serve as a first-line screening tool to rapidly identify clonal clusters of S. marcescens, reducing turnaround time and limiting the number of isolates requiring confirmatory WGS, thereby considerably lowering overall outbreak investigation costs.