Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management

Abstract

Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H₂ O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.

Fig. 1

Second derivative FTIR spectra of four biochemical assigned sub‐ranges of D610 and R125 obtained from 24 h incubation time of MH agar plate. A. Typical infrared spectra in the wavenumber 4000–500 cm⁻¹ of three replicates of D610 (blue line) and R125 (red line); B. Second‐derivative FTIR spectra in the polysaccharide absorption region (1200–900 cm⁻¹); C. Second‐derivative FTIR spectra in the lipids absorption region (3000–2800 cm⁻¹); D. Second‐derivative FTIR spectra in the proteins/amides I and II (1700–1500 cm⁻¹) regions; E. Second‐derivative FTIR spectra in the mixed region of phospholipids/DNA/RNA (1500–1200 cm⁻¹); F. The amplified phospholipids/DNA/RNA region (1425–1250 cm⁻¹).

Fig. 2

Comparison of the results from the two sample preparation methods. A and B represents samples prepared using modified H₂O‐EtOH method and official EtOH‐H₂O method, respectively.

Fig. 3

Cut‐off value assessment of eightK. pneumoniaeisolates. A, B, C represents for strains obtained in three independent days.

Fig. 4

Phylogenetic tree of 17 K. pneumoniaeisolates. The dendrogram was constructed by SNP‐based core‐genome analysis and was rooted by midpoint without branch transform. The lineages of WGS, IRBT, PFGE, and STs are given for each isolate and denoted by colored stripes.

Fig. 5

Phylogenetic tree of 30 outbreak investigationK. pneumoniaeisolates. A dendrogram was obtained by SNP‐based core‐genome analysis and was rooted by midpoint without branch transform. IRBT, Pulsotypes, and STs are given for each isolate and presented as colored stripes. The hospital/patient ID is shown in the text after the corresponding isolate name. Isolates collected from anal swabs were in gray shadow and throat swabs in normal.