GC-IMS Combined with Chemometrics Analysis of Volatile Organic Compounds Facilitates CREC Identification

Abstract

BACKGROUND: Escherichia coli (E. coli) is a clinically significant pathogen. Early identification of carbapenem-resistant E. coli (CREC) is critical for reducing mortality. METHOD: Gas chromatography-ion mobility spectrometry (GC-IMS) combined with chemometric analysis was used to detect volatile organic compounds (VOCs) from 40 clinical E. coli isolates. A two-phase experimental design was implemented: an exploratory phase with six replicates and a validation phase with 40 isolates. Bacteria were cultured in BacT/ALERT^® SA broth, and VOCs were analyzed at specific time points. Imipenem (IPM) was added to induce metabolic stress, whereas pyridine-2,6-dicarboxylic acid (DPA) was used to enhance New Delhi metallo-β-lactamase (NDM)-type CREC discrimination. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were applied to identify key VOCs. RESULTS: GC-IMS analysis revealed 55 VOCs as detectable signals, of which 30 were tentatively identified. In the absence of IPM, only three VOCs showed significant differences between carbapenem-sensitive E. coli (CSEC) and CREC. However, upon the addition of IPM, the number of differentially expressed VOCs increased to 17. PCA and PLS-DA identified 13 key VOCs (including four ketones, two esters, one aldehyde, one pyrazine, and five unknown compounds) that effectively distinguished CSEC from CREC. The addition of DPA further enabled the detection of nine additional VOCs, which may serve as potential markers for identifying NDM-type CREC. CONCLUSION: GC-IMS combined with chemometrics analysis can quickly distinguish CREC from CSEC through analysis of VOC spectra. The addition of IPM and DPA increases metabolic differences, providing a promising method for the rapid detection of CREC.