IR-Biotyper: A New Diagnostic Tool in Microbiology
Résumé
Introduction: Since 2017, human microbiology has seen the rise of the IR-Biotyper (IRBT), using Fourier transform infrared spectrometry. It compares the absorption spectra of surface molecules that vary between strains. IRBT is proposed to group bacterial strains by 1) sequence-type, 2) serotype and clone, facilitating 3) nosocomial and 4) epidemiological surveillance. Already effective for typing Staphylococcus aureus and Klebsiella pneumoniae [1,2], this fast, simple and economical tool could offer an alternative to whole-genome sequencing (WGS) for applications in animal health. Methods: A linear discriminant analysis (LDA), a user-supervised method, were used to analyse the data obtained. The spectra of 125 sequenced (cgMLST) and serotyped Pseudomonas aeruginosa strains were analysed to evaluate the capability of IRBT to group them. Nosocomial surveillance was evaluated with eight Enterobacter hormaechei strains isolated during a microbiological control of a veterinary clinic. Twenty-six Rhodococcus equi strains from eight farms collected over a decade were used to confirm epidemiological surveillance ability. Results: P. aeruginosa strains clustered effectively by sequence type and serotype. In nosocomial surveillance, six beta-lactamase-producing E. hormaechei strains had distinct spectral profiles, except for those from the neonatal unit and operating room, which belong to the same clone. Epidemiological surveillance showed potential clonal strains in three of the eight farms sampled from different horses sampled in the same year. Discussion: Ours promising results confirm the potential of IRBT to characterize strains, consistent with previous literature comparisons of IRBT and WGS [2-4], and for nosocomial and epidemiological surveillance. However, despite reduced variability with LDA, residual differences hinder the visualization of many spectra on a single plot. Standardizing inoculum concentration will improve result clarity and reliability. This innovative tool could bring real-time strain typing within reach!
