Abstract
Members of the Enterobacter (E.) cloacae complex have emerged as important pathogens frequently encountered in nosocomial infections. Several outbreaks with E. cloacae complex have been reported in recent years, especially in neonatal units. Fast and reliable strain typing methods are crucial for real-time surveillance and outbreak analysis to detect pathogen reservoirs and transmission routes. The aim of this study was to evaluate the performance of Fourier-transform infrared (FTIR) spectroscopy as a fast method for typing of clinical E. cloacae complex isolates, when whole genome sequencing (WGS) analysis was used as reference. First, the technique was used retrospectively on 24 first isolates of E. cloacae complex strains from neonatal patients and showed good concordance with SNP-based clustering [adjusted rand index (ARI) = 0.818] and with the sequence type (ST) (ARI = 0.801). 29 consecutive isolates from the same patients were shown by WGS analysis to almost always belong to the same SNP cluster as the first isolates, which was only inconsistently recognized by FTIR spectroscopy. Training of an artificial neural network (ANN) with all FTIR spectra from sequenced strains markedly improved the recognition of related and unrelated isolate spectra. In a second step, FTIR spectroscopy was applied on 14 strains during an outbreak with E. cloacae complex and provided fast typing results that were confirmed by WGS analysis. In conclusion, FTIR spectroscopy is a promising tool for strain typing of clinical E. cloacae complex strains. Discriminatory power can be improved by implementing an ANN for spectrum analysis. Due to its low costs and fast turnaround times, the method presents a valuable tool for real-time surveillance as well as outbreak analysis.
Highlights
The Enterobacter (E.) cloacae complex comprises E. cloacae and several closely related species and subspecies that are difficult to differentiate by standard bacteriological identification methods such as Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) or biochemical profiling (Davin-Regli et al, 2019)
To generate a reference for strain typing results obtained by Fourier-transform infrared (FTIR) spectroscopy, whole genome sequencing (WGS) was performed on the first isolate from each patient
The 24 E. cloacae complex isolates could be assigned to 18 singlenucleotide polymorphism (SNP) clusters, which suggests the presence of a substantial strain diversity found in our NICU patients during a 4-month period
Summary
The Enterobacter (E.) cloacae complex comprises E. cloacae and several closely related species and subspecies that are difficult to differentiate by standard bacteriological identification methods such as Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) or biochemical profiling (Davin-Regli et al, 2019). Fast and reliable strain typing methods of bacterial isolates are crucial to detect possible transmission routes of pathogens and to identify bacterial reservoirs (Li et al, 2009; Sabat et al, 2013) Due to their high discriminatory power, analysis methods that rely on whole genome sequencing (WGS) of bacterial isolates such as singlenucleotide polymorphism (SNP)-based phylogeny calculations and core genome multi-locus sequence typing (cgMLST) or whole genome MLST (wgMLST) are emerging as a gold standard for strain typing. These high-resolution techniques are still time consuming, have relatively high costs per sample, and require substantial computational resources, especially if many isolates must be compared. These techniques are often used retrospectively, but their application in real-time surveillance is still limited (Sabat et al, 2013; Salipante et al, 2015)
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