Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy
Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. <i>Candida</i>...
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doaj-1e28f089ed034e0eae559d2752bc79022020-11-25T02:19:15ZengMDPI AGMolecules1420-30492020-03-01251551155110.3390/molecules25071551Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR SpectroscopySavithri Pebotuwa0Kamila Kochan1Anton Peleg2Bayden R. Wood3Philip Heraud4Department of Microbiology, Monash University, Clayton, Victoria 3800, AustraliaCentre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria 3800, AustraliaInfection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, AustraliaCentre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria 3800, AustraliaCentre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria 3800, AustraliaSeveral studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. <i>Candida</i> species were streaked to obtain colonies and spectra were collected from each preparation type, which included: (a) untreated colonies being directly transferred to the ATR crystal, (b) following washing and (c) following 24-h fixation in formalin. Spectra were pre-processed and principal component analysis (PCA) and K-means cluster analysis (KMC) were performed. Results showed that there was a clear discrimination between preparation types. Groups of spectra from untreated and washed isolates clustered separately due to intense protein, DNA and polysaccharide bands, whilst fixed spectra clustered separately due to intense polysaccharide bands. This signified that sample preparation had influenced the chemical composition of samples. Nevertheless, across preparation types, significant species discrimination was observed, and the polysaccharide (1200–900 cm<sup>−1</sup>) region was a common critical marker for species discrimination. However, different discriminatory marker bands were observed across preparation methods. Thus, sample preparation appears to influence the chemical composition of <i>Candida</i> samples; however, does not seem to significantly impact the species discrimination potential for ATR-FTIR spectroscopy.https://www.mdpi.com/1420-3049/25/7/1551ATR-FTIR spectroscopyfungiPCA<i>Candida</i> |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Savithri Pebotuwa Kamila Kochan Anton Peleg Bayden R. Wood Philip Heraud |
spellingShingle |
Savithri Pebotuwa Kamila Kochan Anton Peleg Bayden R. Wood Philip Heraud Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy Molecules ATR-FTIR spectroscopy fungi PCA <i>Candida</i> |
author_facet |
Savithri Pebotuwa Kamila Kochan Anton Peleg Bayden R. Wood Philip Heraud |
author_sort |
Savithri Pebotuwa |
title |
Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy |
title_short |
Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy |
title_full |
Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy |
title_fullStr |
Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy |
title_full_unstemmed |
Influence of the Sample Preparation Method in Discriminating <i>Candida</i> spp. Using ATR-FTIR Spectroscopy |
title_sort |
influence of the sample preparation method in discriminating <i>candida</i> spp. using atr-ftir spectroscopy |
publisher |
MDPI AG |
series |
Molecules |
issn |
1420-3049 |
publishDate |
2020-03-01 |
description |
Several studies have investigated the capacity of ATR-FTIR spectroscopy for fungal species discrimination. However, preparation methods vary among studies. This study aims to ascertain the effect of sample preparation on the discriminatory capacity of ATR-FTIR spectroscopy. <i>Candida</i> species were streaked to obtain colonies and spectra were collected from each preparation type, which included: (a) untreated colonies being directly transferred to the ATR crystal, (b) following washing and (c) following 24-h fixation in formalin. Spectra were pre-processed and principal component analysis (PCA) and K-means cluster analysis (KMC) were performed. Results showed that there was a clear discrimination between preparation types. Groups of spectra from untreated and washed isolates clustered separately due to intense protein, DNA and polysaccharide bands, whilst fixed spectra clustered separately due to intense polysaccharide bands. This signified that sample preparation had influenced the chemical composition of samples. Nevertheless, across preparation types, significant species discrimination was observed, and the polysaccharide (1200–900 cm<sup>−1</sup>) region was a common critical marker for species discrimination. However, different discriminatory marker bands were observed across preparation methods. Thus, sample preparation appears to influence the chemical composition of <i>Candida</i> samples; however, does not seem to significantly impact the species discrimination potential for ATR-FTIR spectroscopy. |
topic |
ATR-FTIR spectroscopy fungi PCA <i>Candida</i> |
url |
https://www.mdpi.com/1420-3049/25/7/1551 |
work_keys_str_mv |
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