High-throughput diagnosis of pathogenic bacteria

Team: João Lopes, Clara Sousa, João Botelho

Rapid and reliable discrimination among clinically relevant pathogenic organisms is a crucial task in microbiology. Currently used methods for identification and classification of pathogenic organisms can be time consuming and labour intensive, which can hinder the effectiveness of treatment of infections. Fourier Transform Infrared (FT-IR) spectroscopy can be used to assess the overall molecular composition of microbial cells by vibrational spectra that are highly typical for different microorganisms strains and species.
It is a fast, selective, low-cost and non-destructive technique, thus presenting many advantages over existing methods. However, the methodology based on FT-IR requires a somehow complex data processing, still requiring the development of appropriate chemometrics techniques (for the pre-treatment, evaluation, representation and extraction of biochemical information from hyper-spectral data). The use of multivariate data and pattern recognition modelling techniques is necessary to evaluate and compare spectra of thousands of measurements of different species and strains. The major objective is to search for a structure among the observations by maximizing the homogeneity of objects within groups of similar samples while maximizing the heterogeneity between identified groups. Still a major issue in using FT-IR for successful bacteria characterization is the method for spectra pre-processing (removing essentially physical effects such as caused by light scattering but also baseline drift and random noise, that often mask chemical information). The development of a framework for bacteria characterisation based on FT-IR spectroscopy is still a crucial task in order to adopt it as a routine method for clinical, veterinary and environmental diagnosis. With a robust methodology and appropriate databases, the FT-IR system might outperform all actually commercially identification systems with regard to cost and rapidity while preserving performance and reliability. This work aims at establishing a generic methodology or framework for the characterisation of bacteria isolates at different levels (genus, specie, strain, ribopattern or seropatterns and phage type level) using FT-IR. One main advance is to consolidate in a single work the microbiology, spectroscopy and chemometrics perspectives on this subject. Only combining the knowledge on these areas will be possible to achieve the proposed objective.


  • Clara C. Sousa and João A. Lopes. Chapter 20: Infrared spectroscopy detection coupled to chemometrics to characterize foodborne pathogens at a subspecies level, page 385. In: Mathematical and Statistical Approaches in Food Science and Technology. Edited by Daniel Granato and Gáston Ares,IFT Press – Wiley-Blackwell.UK. 2014. (ISBN: 978-1-118-43368-3)
  • Sousa CCS, Grosso F, Meirinhos-Soares L, Peixe L, Lopes JA*, Identification of carbapenem-resistant A. baumannii clones using infrared spectroscopy, J. Biophotonics, in-print
  • Saraiva R, Lopes JA, Feio MJ, Gameiro P*, A novel approach to discriminate E. coli based on its porin expression profile: comparison between ATR and transmission mode FTIR spectroscopy, J. Biophotonics, in-print
  • Sousa C, Silva L, Grosso F, Nemec A, Lopes J, Peixe L. Discrimination of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species by Fourier Transform Infrared Spectroscopy, European Journal of Clinical Microbiology and Infectious Diseases
  • Ângela Novais, Clara Sousa, Juan de Caballero, Ana Fernandez-Olmos, João Lopes, Maria Helena Ramos, Teresa M Coque, Rafael Cantón, Luísa Peixe, MALDI-TOF mass spectrometry as a tool for discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393), European Journal of Clinical Microbiology & Infectious Diseases
  • Clara Sousa, Ângela Novais, Ana Magalhães, João Lopes, and Luisa Peixe, Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy (2013), Sci. Rep., 3, 3278 [doi: 10.1038/srep03278]
  • Vaz MM, Meirinhos-Soares, Sousa CCS, Ramirez M, Melo-Cristino J, Lopes JA* (2013) Serotypes discrimination of encapsulated Streptococcus pneumoniae strains by Fourier-transform infrared spectroscopy and chemometrics, J. Microbiol. Met., 93, 102-107 [doi: 10.1016/j.mimet.2013.02.008]
  • Preisner OE, Menezes JC, Guiomar R, Machado J, Lopes JA* (2012) Discrimination of Salmonella enterica serotypes by Fourier transform infrared spectroscopy, Food Res. Int., 45(2), 1058-1064
  • Preisner OE, Guiomar R, Machado J, Menezes JC and Lopes JA* (2010) Application of Fourier transform infrared spectroscopy and chemometrics for differentiation of Salmonella enterica Serovar Enteritidis phage types, Appl. Environ. Microbiol., 76(11), 3538–3544
  • Coutinho CP, Sá-Correia I, Lopes JA* (2009) Use of Fourier-transform infrared spectroscopy and chemometrics to discriminate clinical isolates of Burkholderia cepacia complex bacteria from different species and ribopatterns, Anal. Bioanal. Chem., 394(8), 2161-2171
  • Preisner OE*, Lopes JA, Guiomar R, Machado J, Menezes JC (2008) Uncertainty assessment in FT-IR spectroscopy based bacteria classification models, Chemom. Intell. Lab. Syst., 94(1), 33-42
  • Preisner OE*, Lopes JA, Giomar R, Machado J, Menezes JC (2007) Fourier transform infrared (FT-IR) spectroscopy in bacteriology: towards a reference method for bacteria discrimination, Anal. Bioanal. Chem., 387, 1739-1748
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