Ann Lab Med.  2023 Mar;43(2):174-179. 10.3343/alm.2023.43.2.174.

Performance Comparison Between Fourier-Transform Infrared Spectroscopy–based IR Biotyper and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Strain Diversity

• Jun SY
• Kim YA
• Lee SJ
• Jung WW
• Kim HS
• Kim SS
• Kim H
• Yong D
• Lee K

• KMID: 2551694
• DOI: http://doi.org/10.3343/alm.2023.43.2.174

Abstract

Background
Development of an accessible method to routinely evaluate the clonality of strains is needed in microbiology laboratories. We compared the discriminatory power of the Fourier-transform infrared (FTIR) spectroscopy–based IR Biotyper (Bruker Daltonics GmbH, Bremen, Germany) to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), using whole-genome sequencing (WGS) as the reference method.
Methods
Eighty-three extended-spectrum β-lactamase–producing Escherichia coli isolates were tested using WGS, MALDI-TOF MS, and IR Biotyper. Simpson’s diversity index (SDI), a statistical analysis for testing the homogeneity of a dendrogram, and the adjusted Rand index (aRI) were used to compare the discriminatory ability between typing tests.
Results
The SDI (95% confidence interval) was 0.969 (0.952–0.985) for WGS, 0.865 (0.807–0.924) for MALDI-TOF MS, and 0.974 (0.965–0.983) for IR Biotyper. Compared with WGS, IR Biotyper showed compatible diversity, whereas MALDI-TOF MS did not. The concordance and aRI improved from 66.3% to 84.3% and from 0.173 to 0.538, respectively, for IR Biotyper versus MALDI-TOF MS with WGS as the reference method. IR Biotyper showed substantially improved performance in strain typing compared with MALDI-TOF MS.
Conclusions
IR Biotyper is useful for diversity analysis with improved discriminatory power over MALDI-TOF MS in comparison with WGS as a reference method. IR Biotyper is an accessible method to evaluate the clonality of strains and could be applied in epidemiological analysis during an outbreak of a health care facility, as well as for research on the transmission of resistant bacteria in community settings.

Keyword

Fourier-transform infrared; Matrix-assisted laser desorption-ionization; Spectrometry; Whole-genome sequencing

Figure

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  Fig. 1 Dendrogram from whole-genome sequencing data created using core-genome multi-locus sequence typing. A total of 83 extended-spectrum-β-lactamase–producing Escherichia coli isolates were determined to have 40 core genome sequence types. The dendrogram was divided largely into three groups.

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  Fig. 2 Dendrogram based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Eighty-three extended-spectrum β-lactamase–producing Escherichia coli isolates were divided into 28 clusters with a distance in the range of 2.0–2.5. Different colors represent separate strains.

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  Fig. 3 Dendrogram and distance matrix obtained by IR Biotyper. (A) Eighty-three strains were classified into 23 groups (A–W); groups S and R were the most similar with a cut-off value (COV) of 0.21 (blue line), whereas groups A and D were the least similar as independent groups with a COV of 0.71. Green indicates a good-quality cluster and orange indicates a poor-quality cluster based on triplicate analyses of each isolate. (B) Distance matrix obtained by IR Biotyper. If the similarity between the two groups was less than 0.39, it was indicated in red, and if it was more than 0.39, it was indicated in blue.

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