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Doh IJ, Zuniga DVS, Shin S, Pruitt RE, Rajwa B, Robinson JP, Bae E. Bacterial Colony Phenotyping with Hyperspectral Elastic Light Scattering Patterns. SENSORS (BASEL, SWITZERLAND) 2023; 23:3485. [PMID: 37050545 PMCID: PMC10098818 DOI: 10.3390/s23073485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The elastic light-scatter (ELS) technique, which detects and discriminates microbial organisms based on the light-scatter pattern of their colonies, has demonstrated excellent classification accuracy in pathogen screening tasks. The implementation of the multispectral approach has brought further advantages and motivated the design and validation of a hyperspectral elastic light-scatter phenotyping instrument (HESPI). The newly developed instrument consists of a supercontinuum (SC) laser and an acousto-optic tunable filter (AOTF). The use of these two components provided a broad spectrum of excitation light and a rapid selection of the wavelength of interest, which enables the collection of multiple spectral patterns for each colony instead of relying on single band analysis. The performance was validated by classifying microflora of green-leafed vegetables using the hyperspectral ELS patterns of the bacterial colonies. The accuracy ranged from 88.7% to 93.2% when the classification was performed with the scattering pattern created at a wavelength within the 473-709 nm region. When all of the hyperspectral ELS patterns were used, owing to the vastly increased size of the data, feature reduction and selection algorithms were utilized to enhance the robustness and ultimately lessen the complexity of the data collection. A new classification model with the feature reduction process improved the overall classification rate to 95.9%.
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Affiliation(s)
- Iyll-Joon Doh
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | | | - Sungho Shin
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Robert E. Pruitt
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - J. Paul Robinson
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Euiwon Bae
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA
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Doh IJ, Kim H, Sturgis J, Rajwa B, Robinson JP, Bae E. Optical multi-channel interrogation instrument for bacterial colony characterization. PLoS One 2021; 16:e0247721. [PMID: 33630969 PMCID: PMC7906345 DOI: 10.1371/journal.pone.0247721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/11/2021] [Indexed: 11/18/2022] Open
Abstract
A single instrument that includes multiple optical channels was developed to simultaneously measure various optical and associated biophysical characteristics of a bacterial colony. The multi-channel device can provide five distinct optical features without the need to transfer the sample to multiple locations or instruments. The available measurement channels are bright-field light microscopy, 3-D colony-morphology map, 2-D spatial optical-density distribution, spectral forward-scattering pattern, and spectral optical density. The series of multiple morphological interrogations is beneficial in understanding the bio-optical features of a bacterial colony and the correlations among them, resulting in an enhanced power of phenotypic bacterial discrimination. To enable a one-shot interrogation, a confocal laser scanning module was built as an add-on to an upright microscope. Three different-wavelength diode lasers were used for the spectral analysis, and high-speed pin photodiodes and CMOS sensors were utilized as detectors to measure the spectral OD and light-scatter pattern. The proposed instrument and algorithms were evaluated with four bacterial genera, Escherichia coli, Listeria innocua, Salmonella Typhimurium, and Staphylococcus aureus; their resulting data provided a more complete picture of the optical characterization of bacterial colonies.
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Affiliation(s)
- Iyll-Joon Doh
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Huisung Kim
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Jennifer Sturgis
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
| | - J. Paul Robinson
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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Buzalewicz I, Karwańska M, Wieliczko A, Podbielska H. On the application of multi-parametric optical phenotyping of bacterial colonies for multipurpose microbiological diagnostics. Biosens Bioelectron 2020; 172:112761. [PMID: 33129071 DOI: 10.1016/j.bios.2020.112761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
The development of new diagnostics techniques and modalities is critical for early detection of microbial contamination. In this study, the novel integrated system for multi-parametric optical phenotyping and characterization of bacterial colonies, is presented. The system combines Mach-Zehnder interferometer with a spectral imaging system for capturing multispectral diffraction patterns and multispectral two-dimensional transmission maps of bacterial colonies, along with the simultaneous interferometric profilometry. The herein presented investigation was carried out on five representative bacteria species and nearly 3000 registered multispectral optical signatures. The interferograms were analyzed by four-step phase shift algorithm to reconstruct the colony profile to enable the obtaining of the comparable optical signatures. The dedicated image processing algorithms were used for extraction of quantitative features of these signatures. The random forest algorithm was applied for selection of the most predictive set of features, which were used in classification model based on Support-Vector Machine. Obtained results have shown that the use of multiple multispectral optical signatures provide a multi-parametric bacteria identification at an exceptionally high accuracy (99.4-100%), significantly better than in case of classification based on each of these signatures (multispectral diffraction patterns, two-dimensional transmission coefficient maps), separately. Obtained results revealed that analysis of multispectral signatures can also be applied for characterisation of physical, physicochemical and chemical properties of the bacterial colonies in the presence of the antimicrobial factors. Therefore, the proposed label-free, non-destructive optical technique has perspectives to be exploited in the multipurpose diagnostics and it can be used as a pre-screening tool in microbiological laboratories.
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Affiliation(s)
- Igor Buzalewicz
- Bio-Optics Group, Department of Biomedical Engineering, Wroclaw University of Science and Technology, 27 Wybrzeze S. Wyspianskiego St., 50-370, Wroclaw, Poland.
| | - Magdalena Karwańska
- Department of Epizootiology and Veterinary Administration with Clinic of Infectious Diseases, Wroclaw University of Environmental and Life Science, 45 Grunwaldzki Square, 50-366, Wroclaw, Poland
| | - Alina Wieliczko
- Department of Epizootiology and Veterinary Administration with Clinic of Infectious Diseases, Wroclaw University of Environmental and Life Science, 45 Grunwaldzki Square, 50-366, Wroclaw, Poland
| | - Halina Podbielska
- Bio-Optics Group, Department of Biomedical Engineering, Wroclaw University of Science and Technology, 27 Wybrzeze S. Wyspianskiego St., 50-370, Wroclaw, Poland
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Development of the Correction Algorithm to Limit the Deformation of Bacterial Colonies Diffraction Patterns Caused by Misalignment and Its Impact on the Bacteria Identification in the Proposed Optical Biosensor. SENSORS 2020; 20:s20205797. [PMID: 33066302 PMCID: PMC7602087 DOI: 10.3390/s20205797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 11/17/2022]
Abstract
Recently proposed methods of bacteria identification in optical biosensors based on the phenomenon of light diffraction on macro-colonies offer over 98% classification accuracy. However, such high accuracy relies on the comparable and repeatable spatial intensity distribution of diffraction patterns. Therefore, it is essential to eliminate all non-species/strain-dependent factors affecting the diffraction patterns. In this study, the impact of the bacterial colony and illuminating beam misalignment on the variation of classification features extracted from diffraction patterns was examined. It was demonstrated that misalignment introduced by the scanning module significantly affected diffraction patterns and extracted classification features used for bacteria identification. Therefore, it is a crucial system-dependent factor limiting the identification accuracy. The acceptable misalignment level, when the accuracy and quality of the classification features are not affected, was determined as no greater than 50 µm. Obtained results led to development of image-processing algorithms for determination of the direction of misalignment and concurrent alignment of the bacterial colonies’ diffraction patterns. The proposed algorithms enable the rigorous monitoring and controlling of the measurement’s conditions in order to preserve the high accuracy of bacteria identification.
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Doh IJ, Sturgis J, Sarria Zuniga DV, Pruitt RE, Robinson JP, Bae E. Generalized spectral light scatter models of diverse bacterial colony morphologies. JOURNAL OF BIOPHOTONICS 2019; 12:e201900149. [PMID: 31386275 DOI: 10.1002/jbio.201900149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/03/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
An optical forward-scatter model was generalized to encompass the diverse nature of bacterial colony morphologies and the spectral information. According to the model, the colony shape and the wavelength of incident light significantly affect the characteristics of a forward elastic-light-scattering pattern. To study the relationship between the colony morphology and the scattering pattern, three-dimensional colony models were generated in various morphologies. The propagation of light passing through the colony model was then simulated. In validation of the theoretical modeling, the scattering patterns of three bacterial genera, Staphylococcus, Exiguobacterium and Bacillus, which grow into colonies having convex, crateriform and flat elevations, respectively, were qualitatively compared to the simulated scattering patterns. The strong correlations observed between simulated and experimental patterns validated the scatter model. In addition, spectral effect on the scattering pattern was studied using the scatter model, and experimentally investigated using Staphylococcus, whose colony has circular form and convex elevation. Both simulation and experiment showed that changes in wavelength affected the overall pattern size and the number of rings.
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Affiliation(s)
- Iyll-Joon Doh
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Jennifer Sturgis
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | | | - Robert E Pruitt
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana
| | - J Paul Robinson
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Euiwon Bae
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
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Acquaro Junior VR, Rodrigues JP, Moraes LAB. Solid phase microextraction as a powerful alternative for screening of secondary metabolites in actinomycetes. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:823-833. [PMID: 31476245 DOI: 10.1002/jms.4434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Actinobacteria are one of the most promising producers of medically and industrially relevant secondary metabolites. However, screening of such compounds in actinobacteria growth demands simple, fast, and efficient extraction procedures that enable detection and precise quantification of biologically active compounds. In this regard, solid phase microextraction (SPME) emerges as an ideal extraction technique for screening of secondary metabolites in bacteria culture due to its non-exhaustive, minimally invasive, and non-destructive nature: its integrated sample preparation workflow; balanced coverage feature; metabolism quenching capabilities; and superior cleanup, as well as its versatility in configuration, which enables automation and high throughput applications. The current work provides a comparison of micro-scale and direct immersion SPME (DI-SPME) for screening of secondary metabolites, describes the optimization of the developed DI-SPME method, and introduces the developed technique for mapping of target secondary metabolites as well as its direct coupling to mass spectrometry for such applications. The optimized DI-SPME method provided higher amounts of extracted ions and intensity signals, yielding superior extraction and desorption efficiency as compared with micro-scale extraction. Studied compounds presented stability on the coating for 24 h at room temperature. The DI-SPME mapping approach revealed that lysolipin I and the lienomycin analog are distributed along the center and edges of the colony, respectively. Direct coupling of SPME to MS provided a similar ions profile as SPME-LC-MS while enabling a significant decrease in analysis time, demonstrating its suitability for such applications. DI-SPME is herein presented as an alternative to micro-scale extraction for screening of secondary metabolites in actinobacteria solid medium, as well as a feasible alternative to DESI-IMS for mapping of biologic radial distribution of secondary metabolites and cell life cycle studies. Lastly, the direct coupling of DI-SPME to MS is presented as a fast, powerful technique for high throughput analysis of secondary metabolites in this medium.
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Affiliation(s)
| | - Júlia Pereira Rodrigues
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Alberto Beraldo Moraes
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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Buzalewicz I, Suchwałko A, Trzciński P, Sas-Paszt L, Sumorok B, Kowal K, Kozera R, Wieliczko A, Podbielska H. Integrated multi-channel optical system for bacteria characterization and its potential use for monitoring of environmental bacteria. BIOMEDICAL OPTICS EXPRESS 2019; 10:1165-1183. [PMID: 30891337 PMCID: PMC6420290 DOI: 10.1364/boe.10.001165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/28/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The potential use of a novel multichannel optical system towards fast and non-destructive bacteria identification and its application for environmental bacteria characterisation on the strain level is presented. It is the first attempt to use the proposed optical method to study various bacteria species (Gram-negative, Gram-positive) commonly present in the environment. The novel configuration of the optical system enables multichannel examination of bacterial colonies and provides additional functionality such as registration of two-dimensional (2D) distribution of monochromatic transmission coefficient of examined colonies, what can be used as a novel optical signature for bacteria characterization. Performed statistical analysis indicates that it is possible to identify representatives of environmental soil bacteria on the species level with the 98.51% accuracy and in case of two strains of Rahnella aquatilis bacteria on the strain level with the 98.8% accuracy. The proposed method is an alternative to the currently used preliminary bacteria examination in environment safety control with the advantage of being fast, reliable, non-destructive and requiring minimal sample preparation.
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Affiliation(s)
- Igor Buzalewicz
- Bio-Optics Group, Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeże S. Wyspiańskiego Street, Wroclaw, Poland
| | | | - Paweł Trzciński
- Rhizosphere Laboratory, Agrotechnical Department, Research Institute of Horticulture, 1/3 Konstytucji 3 Maja Street, Skierniewice, Poland
| | - Lidia Sas-Paszt
- Rhizosphere Laboratory, Agrotechnical Department, Research Institute of Horticulture, 1/3 Konstytucji 3 Maja Street, Skierniewice, Poland
| | - Beata Sumorok
- Rhizosphere Laboratory, Agrotechnical Department, Research Institute of Horticulture, 1/3 Konstytucji 3 Maja Street, Skierniewice, Poland
| | | | - Ryszard Kozera
- Faculty of Applied Informatics and Mathematics, Warsaw University of Life Sciences SGGW, 159 Nowoursynowska Street, Warsaw, Poland
- School of Computer Science and Software Engineering, University of Western Australia, 35 Stirling Highway, WA 6009 Crawley, Perth, Australia
| | - Alina Wieliczko
- Department of Epizootiology and Veterinary Administration with Clinic of Infectious Diseases, Wroclaw University of Environmental and Life Science, 45 Grunwaldzki Square, Wroclaw, Poland
| | - Halina Podbielska
- Bio-Optics Group, Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeże S. Wyspiańskiego Street, Wroclaw, Poland
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Krogsøe K, Henneberg M, Eriksen RL. Model of a Light Extinction Sensor for Assessing Wear Particle Distribution in a Lubricated Oil System. SENSORS 2018; 18:s18124091. [PMID: 30469537 PMCID: PMC6308627 DOI: 10.3390/s18124091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/06/2018] [Accepted: 11/19/2018] [Indexed: 11/25/2022]
Abstract
Light extinction based optical wear particle counters (OPCs) have been widely used in the industry for oil condition monitoring for several years, and while experiments have tested the benefits and drawbacks of the measurement principle, limited research has been conducted regarding a theoretical approach to evaluate opportunities and limitations of the measurement scheme. In this paper, we present a method for theoretically modelling the output of an OPC based on the light extinction principle in the regime of geometrical optics, with a special focus on the influence of sensor optical design, particle concentration and measurement noise. Moreover, we show that, if only signal amplitude is considered, an algorithm for evaluating sensor output can cause an erroneous assessment of particle contamination level.
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Affiliation(s)
- Kevin Krogsøe
- C.C. Jensen A/S, Løvholmen 13, 5700 Svendborg, Denmark.
- SDU Electrical Engineering, The Mads Clausen Institute, Campusvej 55, 5230 Odense M, Denmark.
| | | | - René Lynge Eriksen
- SDU Electrical Engineering, The Mads Clausen Institute, Campusvej 55, 5230 Odense M, Denmark.
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