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

Healthcare-associated infections (HAIs) are a significant concern worldwide due to their impact on patient safety and healthcare costs. Klebsiella spp., particularly Klebsiella pneumoniae and Klebsiella oxytoca, are frequently implicated in HAIs and often exhibit multidrug resistance mechanisms, posing challenges for infection control. In this study, we evaluated Fourier-transform Infrared (FT-IR) spectroscopy as a rapid method for characterizing a nosocomial outbreak caused by VIM-1-producing K. oxytoca. A total of 47 isolates, including outbreak strains and controls, were collected from Hospital Universitario Gregorio Maranon, Spain and the University Hospital Basel, Switzerland. FT-IR spectroscopy was employed for bacterial typing, offering rapid and accurate results compared to conventional methods like pulsed-field gel electrophoresis (PFGE) and correlating with whole-genome sequencing (WGS) results. The FT-IR spectra analysis revealed distinct clusters corresponding to outbreak strains, suggesting a common origin. Subsequent WGS analysis identified Klebsiella michiganensis as the causative agent of the outbreak, challenging the initial assumption based on FT-IR results. However, both FT-IR and WGS methods showed high concordance, with an Adjusted Rand index (AR) of 0.882 and an Adjusted Wallace coefficient (AW) of 0.937, indicating the reliability of FT-IR in outbreak characterization. Furthermore, FT-IR spectra visualization highlighted discriminatory features between outbreak and non-outbreak isolates, facilitating rapid screening in case and outbreak is suspected. In conclusion, FT-IR spectroscopy offers a rapid and cost-effective alternative to traditional typing methods, enabling 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.