Use of Fourier transform infrared spectroscopy and chemometrics to discriminate clinical isolates of bacteria of the Burkholderia cepacia complex from different species and ribopatterns

A methodology for the discrimination of Burkholderia cepacia complex (Bcc) clinical isolates at the species level and at the ribopattern level using Fourier transform infrared (FTIR) spectroscopy and chemometrics analysis was assessed in this study. Different Bcc sequential isolates collected at the Santa Maria Hospital (HSM), in Portugal, from clinically infected cystic fibrosis (CF) patients were previously classified by established molecular methods at the species level and differentiated at the strain level, based on their ribopatterns. A set of 185 of these isolates, representing four different Bcc species (Burkholderia cepacia, Burkholderia cenocepacia (recA lineages III-A and III-B), Burkholderia multivorans and Burkholderia stabilis), was analyzed by FTIR and results were processed with chemometric methods. Ten reference strains of these species were used to test the FTIR method. The discrimination at the species level led to misclassification error rates of 10% and 32% for the HSM isolates and reference strains, respectively, clearly indicating that the FTIR classification method was unable to generalize results for the reference strains. Infrared spectra of HSM isolates were further analyzed in terms of the discrimination according to the ribopattern. Results showed misclassification error rates of 4%, 2%, and 8% for B. cepacia, B. cenocepacia III-A, and B. cenocepacia III-B ribopatterns, respectively. These results demonstrated good FTIR spectroscopy discrimination capacity at the ribopattern level, for the HSM isolates but showed difficulty at the species level, especially when the reference strains were included. Remarkably, this methodology was found to discriminate isolates belonging to the same species and ribopattern that were collected from the same patient during prolonged colonization, opening the door to the identification of chemical modifications resulting from adaptation strategies to the CF lung stressing environment, in particular to aggressive and prolonged antibiotic therapy.