Characterization of a nosocomial outbreak caused by VIM-1 Klebsiella michiganensis using Fourier-Transform Infrared (FT-IR) Spectroscopy.

Abstract

Fourier-transform Infrared (FT-IR) spectroscopy has emerged as a rapid and reliable method for bacterial typing. In this study, we evaluated FT-IR spectroscopy for characterizing a nosocomial outbreak caused by VIM-1-producing Klebsiella michiganensis (K. oxytoca complex). All K. oxytoca complex isolates collected during the outbreak period (N=27) and control isolates (N=8) were obtained from Hospital Universitario Gregorio Marañón, Spain. Among the 27 isolates, 22 were obtained from paediatric patients, 4 from adults and one was an environmental isolate. FT-IR spectroscopy was employed for bacterial typing, while whole-genome sequencing (WGS) was used as the reference typing method for comparison. Analysis of the FT-IR spectra revealed distinct clusters, one of which corresponded to 19 outbreak isolates (18 from paediatric patients and the environmental isolate), suggesting a common origin. Other minor clusters did not exhibit any epidemiological relationship among the isolates. Subsequent WGS analysis identified Klebsiella michiganensis as the causative agent of the outbreak. FT-IR showed a high concordance with WGS in outbreak classification, supporting its reliability in this setting (Adjusted Rand Index=0.882; Adjusted Wallace Coefficient=0.937). Moreover, FT-IR spectra visualization highlighted discriminative features between outbreak and non-outbreak isolates, facilitating rapid screening when an outbreak is suspected. In conclusion, FT-IR spectroscopy represents a rapid and cost-effective method that enables timely intervention and effective management of nosocomial outbreaks. Its integration with WGS enhances the accuracy of outbreak investigations, demonstrating its utility in clinical microbiology and infection control practices.