Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

J Clin Microbiol. 2018 Oct 25;56(11):e00843-18. doi: 10.1128/JCM.00843-18. Print 2018 Nov.

Abstract

Klebsiella pneumoniae and 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 clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains 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 different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due 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 of K. pneumoniae and K. variicola by MALDI-TOF MS.

Keywords: Fourier transform infrared spectroscopy; Klebsiella pneumoniae; Klebsiella variicola; MALDI-TOF mass spectrometry; bacterial typing.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Bacterial Typing Techniques / methods*
  • Bacterial Typing Techniques / standards
  • Cluster Analysis
  • Costs and Cost Analysis
  • Genome, Bacterial / genetics
  • Humans
  • Klebsiella / chemistry
  • Klebsiella / classification*
  • Klebsiella / genetics
  • Klebsiella / isolation & purification*
  • Klebsiella Infections / diagnosis
  • Klebsiella Infections / microbiology*
  • Polymorphism, Single Nucleotide / genetics
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*
  • Spectroscopy, Fourier Transform Infrared*
  • Time Factors