A comparison of multivariate analysis techniques and variable selection strategies in a laser-induced breakdown spectroscopy bacterial classification

Laser-induced breakdown spectroscopy has been used to obtain spectral fingerprints from live bacterial specimens from thirteen distinct taxonomic bacterial classes representative of five bacterial genera. By taking sums, ratios, and complex ratios of measured atomic emission line intensities three unique sets of independent variables (models) were constructed to determine which choice of independent variables provided optimal genus-level classification of unknown specimens utilizing a discriminant function analysis. A model composed of 80 independent variables constructed from simple and complex ratios of the measured emission line intensities was found to provide the greatest sensitivity and specificity. This model was then used in a partial least squares discriminant analysis to compare the performance of this multivariate technique with a discriminant function analysis. The partial least squares discriminant analysis possessed a higher true positive rate, possessed a higher false positive rate, and was more effective at distinguishing between highly similar spectra from closely related bacterial genera. This suggests it may be the preferred multivariate technique in future species-level or strain-level classifications. - Highlights: • Laser-induced breakdown spectroscopy was used to classify bacteria by genus. • We examine three different independent variable down selection models. • A PLS-DA returned higher rates of true positives than a DFA. • A PLS-DA returned higher rates of false positives than a DFA. • A PLS-DA was better able to discriminate similar spectra compared to DFA