Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit

Abstract

The IR Biotyper is a new automated typing system based on Fourier-transform infrared (FT-IR) spectroscopy that gives results within 4 h. We aimed (i) to use the IR Biotyper to retrospectively analyze an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) in a neonatal intensive care unit and to compare results to BOX-PCR and whole-genome sequencing (WGS) results as the gold standard and (ii) to assess how the cutoff values used to define clusters affect the discriminatory power of the IR Biotyper. The sample consisted of 18 isolates from 14 patients. Specimens were analyzed in the IR Biotyper using the default analysis settings, and spectra were analyzed using OPUS 7.5 software. The software contains a feature that automatically proposes a cutoff value to define clusters; the cutoff value defines up to which distance the spectra are considered to be in the same cluster. Based on FT-IR, the outbreak represented 1 dominant clone, 1 secondary clone, and several unrelated clones. FT-IR results, using the cutoff value generated by the accompanying software after 4 replicates, were concordant with WGS for all but 1 isolate. BOX-PCR was underdiscriminatory compared to the other two methods. Using the cutoff value generated after 12 replicates, the results of FT-IR and WGS were completely concordant. The IR Biotyper can achieve the same typeability and discriminatory power as genome-based methods. However, to attain this high performance requires either previous, strain-dependent knowledge about the optimal technical parameters to be used or validation by a second method.

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

“…But from analysis of 8 closely related ST11 isolates, a COV range [0.161, 0.281] obtained can be used to define whether the isolates tested are closely related (strain level for K. pneumoniae); this COV range is similar to the value suggested by the manufacturer [0.2-0.25] for strain-level typing of K. pneumoniae. However, quite different to the results obtained by Rakovitsky, et al (2020), this may due to the different data exploration algorithm, there are several exploration algorithms preloaded in the IRBT system, we select Euclidean distance and average linkage in this study, and Rakovitsky, et al (2020) might use the correlation distance and average linkage, as the quite small COV automatic given by their results. Hence, if the COV range needs to be referenced, we recommend adding the data exploration algorithm.…”

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

“…This study was undertaken to evaluate the applicability of IR Biotyper as a biochemical typing method to type C. auris isolates and compare the outcome with results obtained by MALDI-TOF MS and molecular typing methods. The main goal for the development of the IR Biotyper method was to establish a rapid typing method to investigate the relatedness between isolates involved in nosocomial outbreaks [ 29 , 36 ]. In this study, the five typing approaches, IR Biotyper, MALDI-TOF MS, ITS sequencing, AFLP fingerprinting, and microsatellite typing, did not show concordance.…”

“…The application of this method to type bacterial species in hospital outbreaks was investigated several times. For instance, typing clinical Klebsiella isolates [ 32 , 36 ] and Gram-negative bacilli clones was successfully performed using FTIR spectroscopy (IR Biotyper) [ 37 ]. A few studies have examined the role of FTIR spectroscopy in the typing of clinical isolates [ 38 ].…”

The effect of prophylaxis with ertapenem versus cefuroxime/metronidazole on intestinal carriage of carbapenem-resistant or third-generation-cephalosporin-resistant Enterobacterales after colorectal surgery

“…Clonality was determined using Fourier-transform infrared (FT-IR) spectroscopy [11] on an IR Biotyper (Bruker Daltonik GmbH, Bremen, Germany) according to the manufacturer's instructions. This method detects relatedness of strains by comparing the absorption of infrared light by lipids, proteins, and polysaccharides in the bacterial cell, and has been adopted in recent years as a useful method in hospital epidemiology [12].…”