Fourier transform infrared spectroscopy as a new tool to investigate Clostridioides difficile outbreaks: A proof-of-concept study

Whole genome sequencing (WGS), used as the main method for outbreak investigations, requires substantial technical expertise and is routinely done by reference laboratories. Therefore, the actionable information is often delayed. This study is the first to assess Fourier Transform Infrared (FTIR) spectroscopy as an alternative tool to investigate nosocomial Clostridioides difficile transmission. The FTIR spectroscopy parameters, such as C. difficile growth conditions, FTIR spectroscopy settings and data analysis, were optimized using clonally related C. difficile isolates (n = 5) and epidemiologically unlinked isolates (n = 7). The utility of FTIR to identify clonal relatedness was evaluated using C. difficile isolates (n = 9) from suspected nosocomial transmission events at different hospitals. FTIR spectroscopy results were compared to WGS single nucleotide polymorphism (SNP) analysis. The optimized FTIR protocol correctly clustered clonally related isolates, with clear separation from outgroup isolates. Three C. difficile isolates from an outbreak were identified as one cluster by FTIR whereas 2 isolates from another outbreak were not related based on FTIR results. WGS results corroborated FTIR results in both cases. Additionally, four isolates from suspected patient-to-patient transmission were found to be unrelated by WGS, whereas clustering between some of these isolates was observed by FTIR. FTIR spectroscopy demonstrated good agreement and a high negative predictive value when compared with WGS result. The positive predictive value was lower due to one false positive FTIR cluster of unrelated C. difficile isolates. This proof-of-concept study demonstrated that FTIR spectroscopy is a promising tool for C. difficile outbreak investigations and might be useful to rule-out patient-to-patient transmission.