Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

Meron Ghebremedhin; Shubha Yesupriya; Janos Luka; Nicole J. Crane

doi:10.1117/12.2076997

5 March 2015 Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

Meron Ghebremedhin, Shubha Yesupriya, Janos Luka, Nicole J. Crane

Author Affiliations +

Proceedings Volume 9318, Optical Biopsy XIII: Toward Real-Time Spectroscopic Imaging and Diagnosis; 93180W (2015) https://doi.org/10.1117/12.2076997
Event: SPIE BiOS, 2015, San Francisco, California, United States

Abstract

Recent studies have demonstrated the potential advantages of the use of Raman spectroscopy in the biomedical field due to its rapidity and noninvasive nature. In this study, Raman spectroscopy is applied as a method for differentiating between bacteria isolates for Gram status and Genus species. We created models for identifying 28 bacterial isolates using spectra collected with a 785 nm laser excitation Raman spectroscopic system. In order to investigate the groupings of these samples, partial least squares discriminant analysis (PLSDA) and hierarchical cluster analysis (HCA) was implemented. In addition, cluster analyses of the isolates were performed using various data types consisting of, biochemical tests, gene sequence alignment, high resolution melt (HRM) analysis and antimicrobial susceptibility tests of minimum inhibitory concentration (MIC) and degree of antimicrobial resistance (SIR). In order to evaluate the ability of these models to correctly classify bacterial isolates using solely Raman spectroscopic data, a set of 14 validation samples were tested using the PLSDA models and consequently the HCA models. External cluster evaluation criteria of purity and Rand index were calculated at different taxonomic levels to compare the performance of clustering using Raman spectra as well as the other datasets. Results showed that Raman spectra performed comparably, and in some cases better than, the other data types with Rand index and purity values up to 0.933 and 0.947, respectively. This study clearly demonstrates that the discrimination of bacterial species using Raman spectroscopic data and hierarchical cluster analysis is possible and has the potential to be a powerful point-of-care tool in clinical settings.

Citation Download Citation

Meron Ghebremedhin, Shubha Yesupriya, Janos Luka, and Nicole J. Crane "Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates", Proc. SPIE 9318, Optical Biopsy XIII: Toward Real-Time Spectroscopic Imaging and Diagnosis, 93180W (5 March 2015); https://doi.org/10.1117/12.2076997

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