Discrimination between pathogenic and non-pathogenic E. coli strains by means of Raman microspectroscopy
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Discrimination between pathogenic and non-pathogenic E. coli strains by means of Raman microspectroscopy Björn Lorenz 1,2 & Nairveen Ali 1,3 & Thomas Bocklitz 1,3 & Petra Rösch 1,2
&
Jürgen Popp 1,2,3
Received: 3 July 2020 / Revised: 21 August 2020 / Accepted: 16 September 2020 # The Author(s) 2020
Abstract Bacteria can be harmless commensals, beneficial probiotics, or harmful pathogens. Therefore, mankind is challenged to detect and identify bacteria in order to prevent or treat bacterial infections. Examples are identification of species for treatment of infection in clinics and E. coli cell counting for water quality monitoring. Finally, in some instances, the pathogenicity of a species is of interest. The main strategies to investigate pathogenicity are detection of target genes which encode virulence factors. Another strategy could be based on phenotypic identification. Raman spectroscopy is a promising phenotypic method, which offers high sensitivities and specificities for the identification of bacteria species. In this study, we evaluated whether Raman microspectroscopy could be used to determine the pathogenicity of E. coli strains. We used Raman spectra of seven nonpathogenic and seven pathogenic E. coli strains to train a PCA-SVM model. Then, the obtained model was tested by identifying the pathogenicity of three additional E. coli strains. The pathogenicity of these three strains could be correctly identified with a mean sensitivity of 77%, which is suitable for a fast screening of pathogenicity of single bacterial cells. Keywords E. coli . Pathogen . Identification . Raman microspectroscopy . Bacterium . Single cell
Introduction Bacteria are omnipresent in soil, water, food, and human and animal intestines and on the skin. Although the influence of bacteria on humans is mostly harmless, some bacteria can cause diseases. Two important routes of infection are through food and water. In 2010, foodborne pathogens including viruses caused worldwide 582 million events of foodborne illnesses and resulted in 351 thousand cases of death [1]. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00216-020-02957-2) contains supplementary material, which is available to authorized users. * Petra Rösch [email protected] 1
Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
2
InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena, Germany
3
Leibniz Institute of Photonic Technology Jena Member of the Research Alliance “Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
Consequently, identification of pathogenic bacteria is crucial in the prevention and treatment of infections. Nowadays, culture-based approaches still play a major role in identification of bacteria despite the drawback of long turnaround times, which may reach up to days [2–4]. Some bacteria species are predominantly pathogenic or non-pathogenic. In the case of
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