title: Fourier transform infrared (FT-IR) spectroscopy in bacteriology: towards a reference method for bacteria discrimination.
abstract: Rapid and reliable discrimination among clinically relevant pathogenic organisms is a crucial task in microbiology. Microorganism resistance to antimicrobial agents increases prevalence of infections. The possibility of Fourier transform infrared (FT-IR) spectroscopy to assess the overall molecular composition of microbial cells in a non-destructive manner is reflected in the specific spectral fingerprints highly typical for different microorganisms. With the objective of using FT-IR spectroscopy for discrimination between diverse microbial species and strains on a routine basis, a wide range of chemometrics techniques need to be applied. Still a major issue in using FT-IR for successful bacteria characterization is the method for spectra pre-processing. We analyzed different spectra pre-processing methods and their impact on the reduction of spectral variability and on the increase of robustness of chemometrics models. Different types of the Enterococcus faecium bacterial strain were classified according to chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis (PFGE). Samples were collected from human patients. Collected FT-IR spectra were used to verify if the same classification was obtained. In order to further optimize bacteria classification we investigated whether a selected combination of the most discriminative spectral regions could improve results. Two different variable selection methods (genetic algorithms (GAs) and bootstrapping) were investigated and their relative merit for bacteria classification is reported by comparing with results obtained using the entire spectra. Discriminant partial least-squares (Di-PLS) models based on corrected spectra showed improved predictive ability up to 40% when compared to equivalent models using the entire spectral range. The uncertainty in estimating scores was reduced by about 50% when compared to models with all wavelengths. Spectral ranges with relevant chemical information for Enterococcus faecium bacteria discrimination were outlined.
authors.affiliation: Centre for Biological and Chemical Engineering, IST, Technical University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal. bsel@ist.utl.pt
authors.forename: Ornella
authors.initials: O
authors.lastname: Preisner
authors.forename: João Almeida
authors.initials: JA
authors.lastname: Lopes
authors.forename: Raquel
authors.initials: R
authors.lastname: Guiomar
authors.forename: Jorge
authors.initials: J
authors.lastname: Machado
authors.forename: José C
authors.initials: JC
authors.lastname: Menezes
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods* / Q000592:standards; D001432:Bacteriology; D016002:Discriminant Analysis; D013293:Enterococcus faecalis / Q000737:chemistry* / Q000145:classification / Q000302:isolation & purification*; D016908:Gram-Positive Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology*; D006801:Humans; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013045:Species Specificity; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods* / Q000592:standards