Rapid typing of extended-spectrum β-lactamase- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates by use of SpectraCell RA

Abstract

Enterobacteriaceae are important pathogens of both nosocomial and community-acquired infections. In particular, strains with broad-spectrum beta-lactamases increasingly cause problems in health care settings. Rapid and reliable typing systems are key tools to identify transmission, so that targeted infection control measures can be taken. In this study, we evaluated the performance of Raman spectroscopic analysis (RA) for the typing of multiresistant Escherichia coli and Klebsiella pneumoniae isolates using the SpectraCell RA bacterial strain analyzer (River Diagnostics). Analysis of 96 unrelated isolates revealed that RA generated highly reproducible spectra and exhibited a discriminatory power that is comparable to pulsed-field gel electrophoresis. Furthermore, adequate results were obtained for three collections of clinical isolates. RA was able to discriminate outbreak-related isolates from isolates that were not involved in an outbreak or transmission. Furthermore, it was found that the RA approach recognized clones, irrespective of the extended-spectrum β-lactamase type. It can be concluded that RA is a suitable typing technique for E. coli and K. pneumoniae isolates. Combining high reproducibility, speed, and ease-of-use, this technique may play an important role in monitoring the epidemiology of these important nosocomial species.

Fig 1

Graphical representation of the similarity distributions for K. pneumoniae (A) and E. coli (B). For each species, the distribution of R² values between replicate measurements (red curve) and the distribution of R² values between genetically unrelated isolates (blue curves) are displayed. The similarity threshold and cutoff are indicated by the black doted lines. These lines determine the classification of isolates in three categories of relatedness; unrelated, potentially related, and indistinguishable.

Fig 2

Similarity matrix of the K. pneumoniae isolates from collection II and collection III. Red clusters indicate isolates that are indistinguishable based on the cutoff. The gray areas indicate isolates that are unrelated based on the similarity threshold. The isolates that are potentially related are indicated by yellow to orange. The indicated cluster numbers represent the clusters with indistinguishable isolates based on the cutoff.

Fig 3

Similarity matrix of the E. coli isolates from collection IV. Red clusters indicate isolates that are indistinguishable based on the cutoff. The gray areas indicate isolates that are unrelated based on the similarity threshold. The isolates that are potentially related are indicated by yellow to orange. The indicated cluster numbers represent the clusters with indistinguishable isolates based on the cutoff.