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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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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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Kim H, Rajwa B, Bhunia AK, Robinson JP, Bae E. Development of a multispectral light-scatter sensor for bacterial colonies. JOURNAL OF BIOPHOTONICS 2017; 10:634-644. [PMID: 27412151 DOI: 10.1002/jbio.201500338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/16/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
We report a multispectral elastic-light-scatter instrument that can simultaneously detect three-wavelength scatter patterns and associated optical densities from individual bacterial colonies, overcoming the limits of the single-wavelength predecessor. Absorption measurements on liquid bacterial samples revealed that the spectroscopic information can indeed contribute to sample differentiability. New optical components, including a pellicle beam splitter and an optical cage system, were utilized for robust acquisition of multispectral images. Four different genera and seven shiga toxin producing E. coli serovars were analyzed; the acquired images showed differences in scattering characteristics among the tested organisms. In addition, colony-based spectral optical-density information was also collected. The optical model, which was developed using diffraction theory, correctly predicted wavelength-related differences in scatter patterns, and was matched with the experimental results. Scatter-pattern classification was performed using pseudo-Zernike (GPZ) polynomials/moments by combining the features collected at all three wavelengths and selecting the best features via a random-forest method. The data demonstrate that the selected features provide better classification rates than the same number of features from any single wavelength. Three wavelength-merged scatter pattern from E. coli.
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Affiliation(s)
- Huisung Kim
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Bartek Rajwa
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Arun K Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - J Paul Robinson
- Department of Basic Medical Sciences, 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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Kim H, Doh IJ, Sturgis J, Bhunia AK, Robinson JP, Bae E. Reflected scatterometry for noninvasive interrogation of bacterial colonies. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:107004. [PMID: 27775748 DOI: 10.1117/1.jbo.21.10.107004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 10/06/2016] [Indexed: 06/06/2023]
Abstract
A phenotyping of bacterial colonies on agar plates using forward-scattering diffraction-pattern analysis provided promising classification of several different bacteria such as Salmonella, Vibrio, Listeria, and E. coli. Since the technique is based on forward-scattering phenomena, light transmittance of both the colony and the medium is critical to ensure quality data. However, numerous microorganisms and their growth media allow only limited light penetration and render the forward-scattering measurement a challenging task. For example, yeast, Lactobacillus, mold, and several soil bacteria form colorful and dense colonies that obstruct most of the incoming light passing through them. Moreover, blood agar, which is widely utilized in the clinical field, completely blocks the incident coherent light source used in forward scatterometry. We present a newly designed reflection scatterometer and validation of the resolving power of the instrument. The reflectance-type instrument can acquire backward elastic scatter patterns for both highly opaque media and colonies and has been tested with three different bacterial genera grown on blood agar plates. Cross-validation results show a classification rate above 90% for four genera.
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Affiliation(s)
- Huisung Kim
- Purdue University, School of Mechanical Engineering, Applied Optics Laboratory, West Lafayette, Indiana 47907, United States
| | - Iyll-Joon Doh
- Purdue University, School of Mechanical Engineering, Applied Optics Laboratory, West Lafayette, Indiana 47907, United States
| | - Jennifer Sturgis
- Purdue University, Department of Basic Medical Sciences, West Lafayette, Indiana 47907, United States
| | - Arun K Bhunia
- Purdue University, Molecular Food Microbiology Laboratory, Department of Food Science, West Lafayette, Indiana 47907, United States
| | - J Paul Robinson
- Purdue University, Department of Basic Medical Sciences, West Lafayette, Indiana 47907, United StatesdPurdue University, Weldon School of Biomedical Engineering, West Lafayette, Indiana 47907, United States
| | - Euiwon Bae
- Purdue University, School of Mechanical Engineering, Applied Optics Laboratory, West Lafayette, Indiana 47907, United States
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Buzalewicz I, Kujawińska M, Krauze W, Podbielska H. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography. PLoS One 2016; 11:e0150449. [PMID: 26943121 PMCID: PMC4778909 DOI: 10.1371/journal.pone.0150449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/14/2016] [Indexed: 11/19/2022] Open
Abstract
The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach to the subject.
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Affiliation(s)
- Igor Buzalewicz
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Bio-Optics Group, Wrocław University of Technology, Wrocław, Poland
| | - Małgorzata Kujawińska
- Department of Mechatronics, Institute of Micromechanics and Photonics, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Krauze
- Department of Mechatronics, Institute of Micromechanics and Photonics, Warsaw University of Technology, Warsaw, Poland
| | - Halina Podbielska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Bio-Optics Group, Wrocław University of Technology, Wrocław, Poland
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11
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Interferometry as a tool for evaluating effects of antimicrobial doses on Mycobacterium bovis growth. Tuberculosis (Edinb) 2015; 95:829-838. [DOI: 10.1016/j.tube.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 08/21/2015] [Accepted: 08/26/2015] [Indexed: 11/22/2022]
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Jo Y, Jung J, Kim MH, Park H, Kang SJ, Park Y. Label-free identification of individual bacteria using Fourier transform light scattering. OPTICS EXPRESS 2015; 23:15792-805. [PMID: 26193558 DOI: 10.1364/oe.23.015792] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid identification of bacterial species is crucial in medicine and food hygiene. In order to achieve rapid and label-free identification of bacterial species at the single bacterium level, we propose and experimentally demonstrate an optical method based on Fourier transform light scattering (FTLS) measurements and statistical classification. For individual rod-shaped bacteria belonging to four bacterial species (Listeria monocytogenes, Escherichia coli, Lactobacillus casei, and Bacillus subtilis), two-dimensional angle-resolved light scattering maps are precisely measured using FTLS technique. The scattering maps are then systematically analyzed, employing statistical classification in order to extract the unique fingerprint patterns for each species, so that a new unidentified bacterium can be identified by a single light scattering measurement. The single-bacterial and label-free nature of our method suggests wide applicability for rapid point-of-care bacterial diagnosis.
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Minoni U, Signoroni A, Nassini G. On the application of optical forward-scattering to bacterial identification in an automated clinical analysis perspective. Biosens Bioelectron 2015; 68:536-543. [PMID: 25643595 DOI: 10.1016/j.bios.2015.01.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
The Optical Forward Scattering (OFS) technique can be used to identify pathogens by direct observation of bacteria colonies growing on a culture plate. The identification is based on the acquisition of scattering images from isolated colonies and their subsequent comparison with reference images acquired from known bacteria. The technique has been mainly studied for the identification of pathogens in the food-safety field. This paper focuses on the possibility of extending the applicability of the technique to the field of clinical laboratory automation. This scenario requires that the paradigm of image acquisition at fixed colony-dimension, well established in the food-safety applications, should be substituted by an acquisition at fixed incubation time. As a consequence, the scatterometer must be adjustable in real-time for adapting to the actual features of the bacterial colony. The paper describes an OFS system prototype qualified by the possibility to tune both the laser beam diameter and the acquisition camera field of view. Preliminary experiments on bacteria cultures from pathogens causing infections of the urinary tract show that the proposed approach is promising for the development of an automated bacteria identification station. The new OFS approach also involves an alternative method for building a reference image database for subsequent image analysis.
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Affiliation(s)
- Umberto Minoni
- Department of Information Engineering, University of Brescia, Via Branze 38, I-25133 Brescia, Italy.
| | - Alberto Signoroni
- Department of Information Engineering, University of Brescia, Via Branze 38, I-25133 Brescia, Italy
| | - Giulia Nassini
- Department of Information Engineering, University of Brescia, Via Branze 38, I-25133 Brescia, Italy
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Suchwałko A, Buzalewicz I, Podbielska H. Bacteria identification in an optical system with optimized diffraction pattern registration condition supported by enhanced statistical analysis. OPTICS EXPRESS 2014; 22:26312-26327. [PMID: 25401664 DOI: 10.1364/oe.22.026312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is possible to identify bacteria species basing on their diffraction patterns followed by statistical analysis. The new approach exploits two steps: optimization of the recording conditions and introduction of new interpretable features for the identification. First, optimal diffraction registration plane, was determined. Next, results were verified by the analysis workflow based on ANOVA and Fisher divergence for feature selection, QDA and SVM models for classification and identification and CV with stratified sampling, sensitivity and specificity for performance assessment of the identification process. The proposed approach resulted in high sensitivity 0.9759 and specificity 0.9903 with very small identification error 1.34%.
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Kim H, Singh AK, Bhunia AK, Bae E. Laser-induced speckle scatter patterns in Bacillus colonies. Front Microbiol 2014; 5:537. [PMID: 25352840 PMCID: PMC4196546 DOI: 10.3389/fmicb.2014.00537] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/26/2014] [Indexed: 11/20/2022] Open
Abstract
Label-free bacterial colony phenotyping technology called BARDOT (Bacterial Rapid Detection using Optical scattering Technology) provided successful classification of several different bacteria at the genus, species, and serovar level. Recent experiments with colonies of Bacillus species provided strikingly different characteristics of elastic light scatter (ELS) patterns, which were comprised of random speckles compared to other bacteria, which are dominated by concentric rings and spokes. Since this laser-based optical sensor interrogates the whole volume of the colony, 3-D information of micro- and macro-structures are all encoded in the far-field scatter patterns. Here, we present a theoretical model explaining the underlying mechanism of the speckle formation by the colonies from Bacillus species. Except for Bacillus polymyxa, all Bacillus spp. produced random bright spots on the imaging plane, which presumably dependent on the cellular and molecular organization and content within the colony. Our scatter model-based analysis revealed that colony spread resulting in variable surface roughness can modify the wavefront of the scatter field. As the center diameter of the Bacillus spp. colony grew from 500 to 900 μm, average speckles area decreased two-fold and the number of small speckles increased seven-fold. In conclusion, as Bacillus colony grows, the average speckle size in the scatter pattern decreases and the number of smaller speckle increases due to the swarming growth characteristics of bacteria within the colony.
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Affiliation(s)
- Huisung Kim
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University West Lafayette, IN, USA
| | - Atul K Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University West Lafayette, IN, USA
| | - Arun K Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University West Lafayette, IN, USA
| | - Euiwon Bae
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University West Lafayette, IN, USA
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de Almeida VE, da Costa GB, de Sousa Fernandes DD, Gonçalves Dias Diniz PH, Brandão D, de Medeiros ACD, Véras G. Using color histograms and SPA-LDA to classify bacteria. Anal Bioanal Chem 2014; 406:5989-95. [DOI: 10.1007/s00216-014-8015-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
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Angle-resolved light scattering of individual rod-shaped bacteria based on Fourier transform light scattering. Sci Rep 2014; 4:5090. [PMID: 24867385 PMCID: PMC4035574 DOI: 10.1038/srep05090] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/16/2014] [Indexed: 12/02/2022] Open
Abstract
Two-dimensional angle-resolved light scattering maps of individual rod-shaped bacteria are measured at the single-cell level. Using quantitative phase imaging and Fourier transform light scattering techniques, the light scattering patterns of individual bacteria in four rod-shaped species (Bacillus subtilis, Lactobacillus casei, Synechococcus elongatus, and Escherichia coli) are measured with unprecedented sensitivity in a broad angular range from −70° to 70°. The measured light scattering patterns are analyzed along the two principal axes of rod-shaped bacteria in order to systematically investigate the species-specific characteristics of anisotropic light scattering. In addition, the cellular dry mass of individual bacteria is calculated and used to demonstrate that the cell-to-cell variations in light scattering within bacterial species is related to the cellular dry mass and growth.
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Buzalewicz I, Liżewski K, Kujawińska M, Podbielska H. Degeneration of Fraunhofer diffraction on bacterial colonies due to their light focusing properties examined in the digital holographic microscope system. OPTICS EXPRESS 2013; 21:26493-26505. [PMID: 24216870 DOI: 10.1364/oe.21.026493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The degeneration of Fraunhofer diffraction conditions in the optical system with converging spherical wave illumination for bacteria species identification based on diffraction patterns is analyzed by digital holographic methods. The obtained results have shown that the colonies of analyzed bacteria species act as biological lenses with the time-dependent light focusing properties, which are characterized and monitored by means of phase retrieval from sequentially captured digital holograms. This significantly affects the location of Fraunhofer patterns observation plane, which is continuously shifted across optical axis in time.
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