title: Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy.
abstract: We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from B2(n = 9) and D(n = 13) phylogenetic groups. Eighty-eight E. coli isolates belonging to phylogenetic groups B2(n = 39) and D(n = 49), including particularly widespread high risk clones or clonal complexes (HiRCC) ST131, ST69, ST393 and ST405 were studied. Spectra were analysed by unsupervised (hierarchical cluster analysis-HCA) and supervised methods (soft independent modelling of class analogy-SIMCA and partial least square discriminant analysis-PLSDA). B2-ST131 isolates were discriminated from B2 non-ST131 and D phylogroup isolates (ST69, ST393, ST405) by HCA, SIMCA and PLSDA. D-ST69, D-ST393 and D-ST405 isolates were also distinguished from each other and from other STs from phylogroup D by the three methods. We demonstrate that FTIR-ATR coupled with chemometrics is a reliable and alternative method to accurately discriminate particular E. coli clones. Its validation towards an application at a routine basis could revolutionize high-throughput bacterial typing.
authors.affiliation: REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
authors.forename: Clara
authors.initials: C
authors.lastname: Sousa
authors.forename: Ângela
authors.initials: Â
authors.lastname: Novais
authors.forename: Ana
authors.initials: A
authors.lastname: Magalhães
authors.forename: João
authors.initials: J
authors.lastname: Lopes
authors.forename: Luísa
authors.initials: L
authors.lastname: Peixe
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics; D008962:Models, Theoretical; D010802:Phylogeny; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods