Early identification of a nosocomial outbreak of vancomycin-resistant Enterococcus faecium
Background Early detection of disseminating vancomycin-resistant Enterococcus faecium (VREfm) in ICU wards is crucial for outbreak identification and early response. Genotypic typing methods, such as pulsed-field electrophoresis (PFGE) and whole-genome sequencing (WGS) are expensive, time-consuming and have long time-to-response, mostly since they are batch-dependent. Fourier-transform infrared spectroscopy (FT-IR) for routine monitoring might allow for reliable strain typing and real-time detection of potential outbreaks. We report the use of FT-IR in the identification of a nosocomial outbreak and its performance evaluation compared to PFGE and WGS. Methods From February-May 2023, an unusual number of VREfm were recovered from the haematological ICU. Sixty-six from surveillance swabs and six from clinical samples. AST was determined by disk diffusion and the BD Phoenix™. Carriage of vanA/B genes was determined with GeneXpert® and WGS. Clonality of VREfm was studied prospectively by FT-IR (IR-Biotyper®) using hierarchical analysis on Euclidean average distances. Clonality was also studied retrospectively by PFGE and by WGS (MiSeq™ Illumina®).   Results Routine FT-IR inspection showed recursive clustering of VREfm during the first weeks of the outbreak. 72 isolates were included up to the 31st of May. 59 vanA-positive isolates clustered together constituting the predominant clone. The remaining 13 isolates were classified into 9 FT-IR clusters. Clustering using PFGE and cgMLST (WGS) provided results identical to those of FT-IR; the same number of clusters grouping the same isolates together. WGS corroborated the carriage of vanA/vanB genes and showed the predominant dissemination of a vanA ST80 strain, belonging to CC117. Implementation of infection control measures led to a rapid decline in VREfm isolates during the following months and only 3 isolates were detected in September. Conclusions FT-IR spectroscopy combines fast turnaround times, sensitivity and reproducibility and shows no inferiority to standard and modern typing methods. It is an excellent tool for the routine monitoring of VREfm dissemination and early outbreak detection. Compared to WGS it provides limited yet essential information but at a much lower price and in a faster time-frame.