Typing and Species Identification of ClinicalKlebsiellaIsolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
ABSTRACTKlebsiella pneumoniaeand related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinicalKlebsiellaisolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinicalKlebsiellastrains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for differentKlebsiellaspecies. Phylogenetic analysis revealed that theKlebsiellaisolates comprised three different species:K. pneumoniae,K. variicola, andK. quasipneumoniae. Genome analysis showed that MALDI-TOF MS can be used to distinguishK. pneumoniaefromK. variicoladue to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination ofK. pneumoniaeandK. variicolaby MALDI-TOF MS.