Barcoding bacterial cells: a SERS‐based methodology for pathogen identification
Open accessAbstract
A principal component analysis (PCA) based on the sign of the second derivative of the surface‐enhanced Raman scattering (SERS) spectrum obtained on in situ grown Au‐cluster‐covered SiO 2 substrates results in improved reproducibility and enhanced specificity for bacterial diagnostics. The barcode‐generated clustering results are systematically compared with those obtained from the corresponding spectral intensities, first derivatives and second derivatives for the SERS spectra of closely related cereus group Bacillus strains. PCA plots and the corresponding hierarchical cluster analysis (HCA) dendrograms illustrate the improved bacterial identification resulting from the barcode spectral data reduction. Supervised discriminant function analysis (DFA) plots result in slightly improved group separation but show more susceptibility to false positive classifications than the corresponding PCA contours. In addition, this PCA treatment is used to highlight the enhanced bacterial species specificity observed for SERS as compared to normal bulk (non‐SERS) Raman spectra. The identification algorithm described here is critical for the development of SERS microscopy as a rapid, reagentless and portable diagnostic of bacterial pathogens. Copyright © 2008 John Wiley & Sons, Ltd.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Helgason, E., Økstad, O. A., Caugant, D. A., Johansen, H. A., Fouet, A., Mock, M., Hegna, I. K., & Kolstø, A. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2627-2630.2000 · Cited by 1,072 · see citing works
Microbiological characterizations by FT-IR spectroscopy
Naumann, D., Helm, D., & Labischinski, H. (1991) · Nature · doi:10.1038/351081a0 · Cited by 923 · see citing works
Mock, M., & Fouet, A. (2001) · Annual Review of Microbiology · doi:10.1146/annurev.micro.55.1.647 · Cited by 895 · see citing works
Identification of medically relevant microorganisms by vibrational spectroscopy
Maquelin, K., Kirschner, C., Choo‐Smith, L., van den Braak, N., Endtz, H. P., Naumann, D., & Puppels, G. J. (2002) · Journal of Microbiological Methods · doi:10.1016/s0167-7012(02)00127-6 · Cited by 828 · see citing works
Discrimination of Bacteria Using Surface-Enhanced Raman Spectroscopy
Jarvis, R. M., & Goodacre, R. (2003) · Analytical Chemistry · doi:10.1021/ac034689c · Cited by 637 · see citing works
Demonstration of a capsule plasmid in Bacillus anthracis
Green, B. D., Battisti, L., Koehler, T. M., Thorne, C. B., & Ivins, B. E. (1985) · Infection and Immunity · doi:10.1128/iai.49.2.291-297.1985 · Cited by 491 · see citing works
Characterization of the Surface Enhanced Raman Scattering (SERS) of Bacteria
Premasiri, W. R., Moir, D. T., Klempner, M. S., Krieger, N., Jones, G., & Ziegler, L. D. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp040442n · Cited by 490 · see citing works
Self-citationRaman Microscopic Analysis of Single Microbial Cells
Huang, W. E., Griffiths, R. I., Thompson, I. P., Bailey, M., & Whiteley, A. S. (2004) · Analytical Chemistry · doi:10.1021/ac049753k · Cited by 411 · see citing works
Yonzon, C. R., Haynes, C. L., Zhang, X., Walsh, & Van Duyne, R. P. (2004) · Analytical Chemistry · doi:10.1021/ac035134k · Cited by 376 · see citing works
Maquelin, K., Kirschner, C., Choo‐Smith, L., et al. (2003) · Journal of Clinical Microbiology · doi:10.1128/jcm.41.1.324-329.2003 · Cited by 317 · see citing works
Maquelin, K., Choo‐Smith, L., van Vreeswijk, T., et al. (1999) · Analytical Chemistry · doi:10.1021/ac991011h · Cited by 313 · see citing works
Kirschner, C., Maquelin, K., Pina, P., et al. (2001) · Journal of Clinical Microbiology · doi:10.1128/jcm.39.5.1763-1770.2001 · Cited by 268 · see citing works
Jarvis, R. M., Brooker, A., & Goodacre, R. (2004) · Analytical Chemistry · doi:10.1021/ac049663f · Cited by 236 · see citing works
Surface-enhanced Raman scattering for the rapid discrimination of bacteria
Jarvis, R. M., Brooker, A., & Goodacre, R. (2005) · Faraday Discussions · doi:10.1039/b506413a · Cited by 232 · see citing works
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
Jarvis, R. M., & Goodacre, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti102 · Cited by 181 · see citing works
Naumann, D., Keller, S., Helm, D., Schultz, C., & Schräder, B. (1995) · Journal of Molecular Structure · doi:10.1016/0022-2860(95)08562-a · Cited by 167 · see citing works
Udelhoven, T., Naumann, D., & Schmitt, J. (2000) · Applied Spectroscopy · doi:10.1366/0003702001948619 · Cited by 149 · see citing works
McLean, R. J. C., Beauchemin, D., Clapham, L., & Beveridge, T. J. (1990) · Applied and Environmental Microbiology · doi:10.1128/aem.56.12.3671-3677.1990 · Cited by 144 · see citing works
Convective Assembly of Bacteria for Surface-Enhanced Raman Scattering
Kahraman, M., ÇAĞAL, M. M., Şahi̇n, F., et al. (2008) · Langmuir · doi:10.1021/la702240q · Cited by 142 · see citing works
Rapid Identification ofCandidaSpecies by Confocal Raman Microspectroscopy
Maquelin, K., Choo‐Smith, L., Endtz, H. P., et al. (2002) · Journal of Clinical Microbiology · doi:10.1128/jcm.40.2.594-600.2002 · Cited by 141 · see citing works
Silver metal induced surface enhanced Raman of bacteria
Zeiri, L., Bronk, B. V., Shabtai, Y., et al. (2002) · Colloids and Surfaces A Physicochemical and Engineering Aspects · doi:10.1016/s0927-7757(02)00162-0 · Cited by 140 · see citing works
Shanmukh, S., Jones, L. P., Zhao, Y., et al. (2008) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-008-1851-0 · Cited by 134 · see citing works
Surface-Enhanced Raman Spectroscopy of Bacteria and Pollen
Sengupta, A., Laucks, M. L., & Davis, E. J. (2005) · Applied Spectroscopy · doi:10.1366/0003702054615124 · Cited by 131 · see citing works
Variable Selection in Discriminant Partial Least-Squares Analysis
Alsberg, B. K., Kell, D. B., & Goodacre, R. (1998) · Analytical Chemistry · doi:10.1021/ac980506o · Cited by 120 · see citing works
Laucks, M. L., Sengupta, A., Junge, K., et al. (2005) · Applied Spectroscopy · doi:10.1366/000370205774430891 · Cited by 108 · see citing works
Kahraman, M., ÇAĞAL, M. M., Slahin, F., et al. (2007) · Applied Spectroscopy · doi:10.1366/000370207780807731 · Cited by 106 · see citing works
Pomerantsev, A. P., Kalnin, K. V., Osorio, M., et al. (2003) · Infection and Immunity · doi:10.1128/iai.71.11.6591-6606.2003 · Cited by 89 · see citing works
Hutsebaut, D., Maquelin, K., Vos, P. D., et al. (2004) · Analytical Chemistry · doi:10.1021/ac049228l · Cited by 61 · see citing works
SERS of whole-cell bacteria and trace levels of biological molecules
Guzelian, A. A., Sylvia, J. M., Janni, J. A., et al. (2002) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.455736 · Cited by 43 · see citing works
Synthesis and characterization of SERS gene probe for BRCA-1 (breast cancer)
Pal, A., Isola, N. R., Alarie, J. P., Stokes, D. L., & Vo‐Dinh, T. (2005) · Faraday Discussions · doi:10.1039/b506341h · Cited by 37 · see citing works
Plasmonics-Based Nanostructures for Surface-Enhanced Raman Scattering Bioanalysis
Vo‐Dinh, T., Yan, F., & Stokes, D. L. (2005) · Humana Press eBooks · doi:10.1385/1-59259-858-7:255 · Cited by 30 · see citing works
Vibrational fingerprinting of bacterial pathogens by surface enhanced Raman scattering (SERS)
Premasiri, W. R., Moir, D. T., & Ziegler, L. D. (2005) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.605742 · Cited by 20 · see citing works
Self-citationSurface-Enhanced Raman Scattering of Microorganisms
Premasiri, W. R., Moir, D. T., Klempner, M. S., et al. (2007) · ACS symposium series · doi:10.1021/bk-2007-0963.ch012 · Cited by 19 · see citing works
Self-citationSurface-enhanced Raman spectroscopy of bacteria coated by silver
Efrima, S., Bronk, B. V., & Czégé, J. (1999) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.347519 · Cited by 13 · see citing works
Optimization of substrates for surface-enhanced Raman spectroscopy of bacteria
Fell, N. F., Smith, A. G. B., Vellone, M., et al. (2002) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.455735 · Cited by 12 · see citing works
Markers and methods for biodetection
Fox, A. (2006) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.650727 · Cited by 4 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [1]Vo-Dinh T Yan F Stokes DL Methods Mol Biol 300 255 83 2005 15657488
Cited by
Sorted by citations
Li, J. Q., Dukes, P. V., Lee, W., Sarkis, M., & Vo‐Dinh, T. (2022) · Journal of Raman Spectroscopy · doi:10.1002/jrs.6447 · Cited by 78 · see citing works
Ding, J., Lin, Q., Zhang, J., Young, G. M., Jiang, C., Zhong, Y., & Zhang, J. (2021) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-021-03332-5 · Cited by 61 · see citing works
- Authors
- Patel, I. S., Premasiri, W. R., Moir, D. T., & Ziegler, L. D.
- Affiliations
- Boston University (US)
- Microbiotix (United States) (US)
- Corresponding author
- Ziegler, L. D.
- Venue
- Journal of Raman Spectroscopy
- Publisher
- Wiley
- Published
- 2008-10-17
- Volume
- 39
- Issue
- 11
- Pages
- 1660-1672
- ISSN
- 0377-0486 (ISSN-L)
- 1097-4555
- PMC
- PMC2732026
- OpenAlex
- W2003515234
- Cited by
- 207
- References
- 36
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 10 · 2023: 13 · 2022: 4 · 2021: 9 · 2020: 11 · 2019: 6 · 2018: 13 · 2017: 23 · 2016: 14 · 2015: 15 · 2014: 11 · 2013: 9 · 2012: 20
- FWCI
- 7.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Raman Spectroscopy (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases (R41AI066641)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Spectroscopy Techniques in Biomedical and Chemical Research
- Physical Sciences › Materials Science › Electronic, Optical and Magnetic Materials › Gold and Silver Nanoparticles Synthesis and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- surface-enhanced Raman spectroscopy, bacterial identification, second derivative spectra, principal component analysis, Bacillus cereus group, spectral data reduction, hierarchical clustering, discriminant analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
