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 AE 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 H 2 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.

Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy

“…lactis . Although the functionality of FTIR method in species typing has been already verified for Gram-negative bacteria, such as E. coli , Klebsiella oxytoca , and Y. enterocolitica ( Kuhm et al, 2009 ; Sousa et al, 2013 ; Dieckmann et al, 2016 ), and isolates responsible for hospital outbreaks, such as Enterobacter cloacae , K. pneumoniae , and Pseudomonas aeruginosa ( Martak et al, 2019 ; Hu et al, 2020 ), its discriminatory power has not been assessed for Gram-positive and probiotic bacteria until now.…”

“…Several studies using FTIR spectroscopy focused on foodborne, clinical, and epidemiological pathogens, e.g., Escherichia coli , Salmonella enterica , Streptococcus pneumoniae , and Listeria monocytogenes ( Preisner et al, 2010 ; Fetsch et al, 2014 ; Nyarko et al, 2014 ; Novais et al, 2019 ), and have recently paved the way for outbreak investigation ( Martak et al, 2019 ; Hu et al, 2020 ). Particularly, as FTIR was broadly explored for bacterial classification at the species level, it was also proposed for bacterial typing at the subspecies level, aiming to find an alternative to the established, but very expensive, time-consuming and not applicable on large-scale DNA-based techniques and other methods with high discriminatory power commonly used for epidemiological purposes.…”

“…The main advantages related to this method are the analysis time, cost, laboratorial simplicity, absence of chemical reagents, and very low sample amount per analysis, in addition to relevant information about the biomolecular content of the microorganisms including lipids, carbohydrates, proteins, and nucleic acids deriving from the IR spectrum ( Quintelas et al, 2018 ). In 2018, Bruker commercialized an automated typing system based on FTIR technology, the IR Biotyper (Bruker GmbH, Bremen, Germany), whose application has gained large interest, becoming common in typing bacterial isolates especially in the field of clinical microbiology ( Bruker GmbH Daltonics Division, 2018 ; Burckhardt et al, 2019 ; Martak et al, 2019 ; Hu et al, 2020 ).…”

Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy

“…FTIRS has been successfully applied in many studies for the discrimination of bacteria at different taxonomic levels (genera, species, serogroup/type, and even at strain level). So far, it has been proven to be a simple, quick, high-throughput and cost-effective bacterial typing technique [46][47][48][49][50][51][52].…”

New advances into antimicrobial research

“…Liu et al ., 2021 ), microbial contamination prevention in plants (Taylor et al ., 2021 ), laboratory aspects and the clinical use of antimicrobials (i.e. Hu et al ., 2021 ).…”