Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characteriseEnterobacter cloacae, Citrobacter freundiiandKlebsiella pneumoniaeisolates recovered from hospital sinks

Abstract

2.AbstractWhole genome sequencing (WGS) of healthcare-associated pathogens is recognised as the gold standard for isolate typing and the recognition of transmission networks and outbreaks. However, it remains reasonably expensive to process small numbers of isolates in real-time, and frequently requires specific expertise to enable both sequencing and the analysis of sequencing outputs, limiting its generalisability and turnaround. Spectrometry has revolutionised species identification in clinical laboratory workflows, and has more recently been applied to strain-level identification to facilitate low-cost, routine strain typing in clinical laboratories. However, studies to date of its clinical performance for strain-level typing are conflicting, and limited evaluation has been undertaken on environmental healthcare-associated isolates. We therefore compared its performance with WGS forEnterobacter cloacae, Citrobacter freundiiandKlebsiella pneumoniaeisolated from sink drains across nine hospitals and investigated whether it could be used as a screening tool prior to WGS. We found its sensitivity and specificity to cluster isolates when compared with WGS were generally poor and highly variable dependent on species and the single nucleotide polymorphism (SNP) distance threshold used to cluster isolates.3.Impact statementEnterobacterales are key pathogens of concern in healthcare-associated infections and have been shown to be disseminated via environmental reservoirs in hospitals. Accurately evaluating strain-based transmission networks amongst patients and hospital environments is critical to optimising infection prevention and control interventions. The current gold standard approach to characterise these transmission networks is to use genome sequencing of isolates, but this remains expensive and challenging to do routinely in many clinical laboratories.Bacterial characterisation based on protein spectra has been widely implemented for species identification in diagnostic microbiology, and devices such as Bruker’s matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry system (MALDI Biotyper) have revolutionised workflows, reducing both costs and turnaround. Bruker have introduced another device, known as the IR Biotyper, which aims to use infrared spectroscopy to characterise strain-level variability and facilitate outbreak investigation. Our study shows that when compared to whole genome sequencing, the IR Biotyper cannot be used reliably to type collections of isolates collected from the hospital sink environment, which might limit its suitability to investigate outbreaks associated with this environmental reservoir.4.Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.Raw isolate sequencing data are deposited in NCBI (BioProject accession: PRJNA925315).Supplementary data files, phylogenetic and IR Biotyper trees are deposited in Figsharehttps://doi.org/10.6084/m9.figshare.22016009.v1