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Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis
T C Scheier1, J Franz1, M Boumasmoud1,2
1Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich , Zurich, Switzerland.
Importance:
Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.
Insights
Fourier-transform infrared (FT-IR) spectroscopy offers a rapid and affordable method for investigating vancomycin-resistant Enterococci (VREfm) outbreaks. This technique shows high agreement with whole genome sequencing, proving effective for bacterial typing in clinical settings.
Area of Science:
- Microbiology
- Infectious Diseases
- Spectroscopy
Background:
- Vancomycin-resistant Enterococci, primarily Enterococcus faecium (VREfm), are significant causes of hospital-acquired infections and outbreaks.
- Current bacterial typing methods for outbreak investigations, such as MLST and WGS, are often costly and time-consuming.
- There is a need for accessible, rapid, and reliable methods for VREfm typing to aid in infection control.
Purpose of the Study:
- To evaluate the efficacy of Fourier-transform infrared (FT-IR) spectroscopy as a tool for investigating vancomycin-resistant Enterococci (VREfm) outbreaks.
- To assess the performance characteristics of FT-IR spectroscopy, including reproducibility and the impact of incubation time.
- To compare the discriminatory power and clustering agreement of FT-IR spectroscopy with established methods like whole genome sequencing (WGS) and multi-locus sequence typing (MLST).
Main Methods:
- Basic performance assessments of FT-IR spectroscopy were conducted, evaluating reproducibility and the effect of incubation time on distinct sample sets.
- A cut-off range for FT-IR spectroscopy was determined.
- Clustering agreement between FT-IR spectroscopy and WGS (using an Average Nucleotide Identity cut-off of 0.999) was investigated in retrospective (n=92 isolates) and prospective (n=15 isolates) outbreak datasets.
Main Results:
- Basic performance analysis demonstrated reproducible results for FT-IR spectroscopy.
- FT-IR spectroscopy showed a high agreement with WGS-ANI analysis in clinical outbreak investigations, with V-measures of 0.772 for the retrospective and 1.000 for the prospective outbreak.
- FT-IR spectroscopy exhibited higher discriminatory power compared to MLST in outbreak investigations.
Conclusions:
- FT-IR spectroscopy is a promising, affordable, and easy-to-use technique for VREfm outbreak investigations, offering a turnaround time of less than one day.
- The method demonstrates high agreement with WGS-based typing and superior discriminatory power over MLST.
- With established cut-off values, FT-IR spectroscopy can effectively assist in species discrimination and outbreak analysis.
