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Narayana Iyengar S, Dowden B, Ragheb K, Patsekin V, Rajwa B, Bae E, Robinson JP. Identifying antibiotic-resistant strains via cell sorting and elastic-light-scatter phenotyping. Appl Microbiol Biotechnol 2024; 108:406. [PMID: 38958764 PMCID: PMC11222266 DOI: 10.1007/s00253-024-13232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 07/04/2024]
Abstract
The proliferation and dissemination of antimicrobial-resistant bacteria is an increasingly global challenge and is attributed mainly to the excessive or improper use of antibiotics. Currently, the gold-standard phenotypic methodology for detecting resistant strains is agar plating, which is a time-consuming process that involves multiple subculturing steps. Genotypic analysis techniques are fast, but they require pure starting samples and cannot differentiate between viable and non-viable organisms. Thus, there is a need to develop a better method to identify and prevent the spread of antimicrobial resistance. This work presents a novel method for detecting and identifying antibiotic-resistant strains by combining a cell sorter for bacterial detection and an elastic-light-scattering method for bacterial classification. The cell sorter was equipped with safety mechanisms for handling pathogenic organisms and enabled precise placement of individual bacteria onto an agar plate. The patterning was performed on an antibiotic-gradient plate, where the growth of colonies in sections with high antibiotic concentrations confirmed the presence of a resistant strain. The antibiotic-gradient plate was also tested with an elastic-light-scattering device where each colony's unique colony scatter pattern was recorded and classified using machine learning for rapid identification of bacteria. Sorting and patterning bacteria on an antibiotic-gradient plate using a cell sorter reduced the number of subculturing steps and allowed direct qualitative binary detection of resistant strains. Elastic-light-scattering technology is a rapid, label-free, and non-destructive method that permits instantaneous classification of pathogenic strains based on the unique bacterial colony scatter pattern. KEY POINTS: • Individual bacteria cells are placed on gradient agar plates by a cell sorter • Laser-light scatter patterns are used to recognize antibiotic-resistant organisms • Scatter patterns formed by colonies correspond to AMR-associated phenotypes.
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Affiliation(s)
| | - Brianna Dowden
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Kathy Ragheb
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Valery Patsekin
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Euiwon Bae
- School of Mechanical Engineering, 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.
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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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3
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Wu X, Shin S, Gondhalekar C, Patsekin V, Bae E, Robinson JP, Rajwa B. Rapid Food Authentication Using a Portable Laser-Induced Breakdown Spectroscopy System. Foods 2023; 12:402. [PMID: 36673494 PMCID: PMC9857504 DOI: 10.3390/foods12020402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/13/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Laser-induced breakdown spectroscopy (LIBS) is an atomic-emission spectroscopy technique that employs a focused laser beam to produce microplasma. Although LIBS was designed for applications in the field of materials science, it has lately been proposed as a method for the compositional analysis of agricultural goods. We deployed commercial handheld LIBS equipment to illustrate the performance of this promising optical technology in the context of food authentication, as the growing incidence of food fraud necessitates the development of novel portable methods for detection. We focused on regional agricultural commodities such as European Alpine-style cheeses, coffee, spices, balsamic vinegar, and vanilla extracts. Liquid examples, including seven balsamic vinegar products and six representatives of vanilla extract, were measured on a nitrocellulose membrane. No sample preparation was required for solid foods, which consisted of seven brands of coffee beans, sixteen varieties of Alpine-style cheeses, and eight different spices. The pre-processed and standardized LIBS spectra were used to train and test the elastic net-regularized multinomial classifier. The performance of the portable and benchtop LIBS systems was compared and described. The results indicate that field-deployable, portable LIBS devices provide a robust, accurate, and simple-to-use platform for agricultural product verification that requires minimal sample preparation, if any.
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Affiliation(s)
- Xi Wu
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sungho Shin
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Carmen Gondhalekar
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Valery Patsekin
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Euiwon Bae
- School of Mechanical Engineering, 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
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
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Bhunia AK, Singh AK, Parker K, Applegate BM. Petri-plate, bacteria, and laser optical scattering sensor. Front Cell Infect Microbiol 2022; 12:1087074. [PMID: 36619754 PMCID: PMC9813400 DOI: 10.3389/fcimb.2022.1087074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Classical microbiology has paved the path forward for the development of modern biotechnology and microbial biosensing platforms. Microbial culturing and isolation using the Petri plate revolutionized the field of microbiology. In 1887, Julius Richard Petri invented possibly the most important tool in microbiology, the Petri plate, which continues to have a profound impact not only on reliably isolating, identifying, and studying microorganisms but also manipulating a microbe to study gene expression, virulence properties, antibiotic resistance, and production of drugs, enzymes, and foods. Before the recent advances in gene sequencing, microbial identification for diagnosis relied upon the hierarchal testing of a pure culture isolate. Direct detection and identification of isolated bacterial colonies on a Petri plate with a sensing device has the potential for revolutionizing further development in microbiology including gene sequencing, pathogenicity study, antibiotic susceptibility testing , and for characterizing industrially beneficial traits. An optical scattering sensor designated BARDOT (bacterial rapid detection using optical scattering technology) that uses a red-diode laser, developed at the beginning of the 21st century at Purdue University, some 220 years after the Petri-plate discovery can identify and study bacteria directly on the plate as a diagnostic tool akin to Raman scattering and hyperspectral imaging systems for application in clinical and food microbiology laboratories.
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Affiliation(s)
- Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States,*Correspondence: Arun K. Bhunia,
| | - Atul K. Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Clear Labs, San Carlos, CA, United States
| | - Kyle Parker
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Bruce M. Applegate
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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5
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Tetz G, Tetz V. Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection. Microorganisms 2022; 10:2383. [PMID: 36557636 PMCID: PMC9781420 DOI: 10.3390/microorganisms10122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY 100141, USA
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Doh IJ, Dowden B, Patsekin V, Rajwa B, Robinson JP, Bae E. Development of a Smartphone-Integrated Reflective Scatterometer for Bacterial Identification. SENSORS (BASEL, SWITZERLAND) 2022; 22:2646. [PMID: 35408260 PMCID: PMC9003293 DOI: 10.3390/s22072646] [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: 02/10/2022] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
We present a smartphone-based bacterial colony phenotyping instrument using a reflective elastic light scattering (ELS) pattern and the resolving power of the new instrument. The reflectance-type device can acquire ELS patterns of colonies on highly opaque media as well as optically dense colonies. The novel instrument was built using a smartphone interface and a 532 nm diode laser, and these essential optical components made it a cost-effective and portable device. When a coherent and collimated light source illuminated a bacterial colony, a reflective ELS pattern was created on the screen and captured by the smartphone camera. The collected patterns whose shapes were determined by the colony morphology were then processed and analyzed to extract distinctive features for bacterial identification. For validation purposes, the reflective ELS patterns of five bacteria grown on opaque growth media were measured with the proposed instrument and utilized for the classification. Cross-validation was performed to evaluate the classification, and the result showed an accuracy above 94% for differentiating colonies of E. coli, K. pneumoniae, L. innocua, S. enteritidis, and S. aureus.
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Affiliation(s)
- Iyll-Joon Doh
- Applied Optics Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA;
| | - Brianna Dowden
- Basic Medical Science, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (B.D.); (V.P.); (J.P.R.)
| | - Valery Patsekin
- Basic Medical Science, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (B.D.); (V.P.); (J.P.R.)
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA;
| | - J. Paul Robinson
- Basic Medical Science, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (B.D.); (V.P.); (J.P.R.)
- 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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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Kim YH, Park PG, Seo SH, Hong KJ, Youn H. Development of dual reporter imaging system for Francisella tularensis to monitor the spatio-temporal pathogenesis and vaccine efficacy. Clin Exp Vaccine Res 2018; 7:129-138. [PMID: 30112352 PMCID: PMC6082674 DOI: 10.7774/cevr.2018.7.2.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/02/2018] [Indexed: 11/17/2022] Open
Abstract
Purpose Study on the pathogen and the pathogen-related disease require the information at both cellular and organism level. However, lack of appropriate high-quality antibodies and the difference between the experimental animal models make it difficult to analyze in vivo mechanism of pathogen-related diseases. For more reliable research on the infection and immune-response of pathogen-related diseases, accurate analysis is essential to provide spatiotemporal information of pathogens and immune activity to avoid false-positive or mis-interpretations. In this regards, we have developed a method for tracking Francisella tularensis in the animal model without using the specific antibodies for the F. tularensis. Materials and Methods A dual reporter plasmid using GFP-Lux with putative bacterioferritin promoter (pBfr) was constructed and transformed to F. tularensis live vaccine strain to generate F. tularensis LVS (FtLVS)-GFP-Lux for both fluorescence and bioluminescence imaging. For vaccination to F. tularensis infection, FtLVS and lipopolysaccharide (LPS) from FtLVS were used. Results We visualized the bacterial replication of F. tularensis in the cells using fluorescence and bioluminescence imaging, and traced the spatio-temporal process of F. tularensis pathogenesis in mice. Vaccination with LPS purified from FtLVS greatly reduced the bacterial replication of FtLVS in animal model, and the effect of vaccination was also successfully monitored with in vivo imaging. Conclusion We successfully established dual reporter labeled F. tularensis for cellular and whole body imaging. Our simple and integrated imaging analysis system would provide useful information for in vivo analysis of F. tularensis infection as well as in vitro experiments, which have not been fully explained yet with various technical problems.
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Affiliation(s)
- Young-Hwa Kim
- Department of Nuclear Medicine, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Pil-Gu Park
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | | | - Kee-Jong Hong
- Interpark Bio-Convergence Center, I-Market-Korea, Seoul, Korea
| | - Hyewon Youn
- Department of Nuclear Medicine, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Cancer Imaging Center, Seoul National University Hospital, Seoul, Korea
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10
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Vanegas DC, Gomes CL, Cavallaro ND, Giraldo‐Escobar D, McLamore ES. Emerging Biorecognition and Transduction Schemes for Rapid Detection of Pathogenic Bacteria in Food. Compr Rev Food Sci Food Saf 2017; 16:1188-1205. [DOI: 10.1111/1541-4337.12294] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Diana C. Vanegas
- Food Engineering Univ. del Valle 338 Ciudad Universitaria Meléndez Cali Colombia
| | - Carmen L. Gomes
- Biological & Agricultural Engineering Texas A&M Univ. 2117 TAMU, Scoates Hall 201 College Station TX 77843 U.S.A
| | - Nicholas D. Cavallaro
- Agricultural & Biological Engineering Univ. of Florida 1741 Museum Rd Gainesville FL 32606 U.S.A
| | | | - Eric S. McLamore
- Agricultural & Biological Engineering Univ. of Florida 1741 Museum Rd Gainesville FL 32606 U.S.A
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11
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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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12
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Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 2017; 14:296-310. [PMID: 28248946 PMCID: PMC5473291 DOI: 10.1038/nrurol.2017.20] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.
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Affiliation(s)
- Michael Davenport
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Linda M Dairiki Shortliffe
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, California 94304 USA
| | - Tza-Huei Wang
- Departments of Mechanical and Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304 USA
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13
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Zhang W, Zhu L, Zhang F, Lou X, Liu C, Meng X. Evaluating the liquid path stability of a flow cytometer. Cytometry A 2016; 89:941-948. [PMID: 27632708 DOI: 10.1002/cyto.a.22978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/11/2022]
Abstract
Precision in flow cytometry depends on many factors, the first of which is accurate and stable positioning of the hydrodynamically focused cells. However, no method exists to evaluate the stability of laminar flow and single-cell flow in the flow chamber of the flow cytometer directly because of the small size of the rectangular channel of the flow chamber. In this paper, a method of high-speed particle image velocimetry is proposed to solve this problem. The velocity stability of the particles in the flow chamber is used to evaluate the flow stability of the fluid path of the flow cytometer. The side scattering images of particles are obtained by a high-speed camera. Upon exposure, cells were imaged at random positions in the flow cell, resulting in four different types of the images: blank, inadequate, normal, or overlapped. Normal images were identified utilizing a grey cluster analysis algorithm based on trapezoid whitenization weight functions. A mid-point method is applied to determine the length of the particle track at a fixed exposure time. The variation of the trajectory lengths of the normal images are used to evaluate the stability of the liquid path. Experiments are carried out to verify the feasibility of our method in which different diameter microspheres at different flow rates. The results indicate that the standard deviation and relative standard deviation of the trajectory lengths can be used as the evaluation indices of the liquid path stability of the flow cytometer. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Wenchang Zhang
- School of Instrumentation Science & Opto-Electronics Engineering, Hefei University of Technology, Hefei, 230009, China.,Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China.,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China
| | - Lianqing Zhu
- Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China. .,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China.
| | - Fan Zhang
- Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China.,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China
| | - Xiaoping Lou
- Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China.,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China
| | - Chao Liu
- Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China.,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China
| | - Xiaochen Meng
- Beijing Key Laboratory for Optoelectronics Measurement Technology, Beijing Information Science and Technology University, Beijing, 100192, China.,Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing Information Science and Technology University, Beijing, 100192, China
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14
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Connell S, Li J, Durkes A, Zaroura M, Shi R. Nondermal irritating hyperosmotic nanoemulsions reduce treatment times in a contamination model of wound healing. Wound Repair Regen 2016; 24:669-78. [DOI: 10.1111/wrr.12436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/01/2016] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jianming Li
- Medtric Biotech, LLCWest Lafayette Indiana
- Center for Paralysis Research, Purdue UniversityWest Lafayette Indiana47907
| | - Abigail Durkes
- Comparative Pathobiology Department, College of Veterinary MedicinePurdue UniversityWest Lafayette Indiana47907
| | | | - Riyi Shi
- Department of Basic Medical Sciences, College of Veterinary MedicinePurdue UniversityWest Lafayette Indiana47907
- Weldon School of Biomedical Engineering, College of EngineeringPurdue UniversityWest Lafayette Indiana
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15
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Myer PR, Parker KR, Kanach AT, Zhu T, Morgan MT, Applegate BM. The effect of a novel low temperature-short time (LTST) process to extend the shelf-life of fluid milk. SPRINGERPLUS 2016; 5:660. [PMID: 27350902 PMCID: PMC4899401 DOI: 10.1186/s40064-016-2250-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/28/2016] [Indexed: 11/12/2022]
Abstract
Pasteurization has long been the standard method to extend the shelf-life of dairy products, as well as a means to reduce microbial load and the risk of food-borne pathogens. However, the process has limitations, which include cost effectiveness, high energy input, and reduction of product quality/organoleptic characteristics. In an effort to reduce these limitations and extend shelf-life, this study examined a novel low temperature, short time (LTST) method in which dispersed milk in the form of droplets was treated with low heat/pressure variation over a short treatment time, in conjunction with pasteurization. Lactobacillus fermentum and Pseudomonas fluorescens Migula were exposed to conventional pasteurization treatments with and without LTST. Using these organisms, the LTST addition was able to reduce microbial load below detection limits; 1.0 × 101 cfu/mL, from approximately 1.2 × 108 and 1.0 × 107 cfu/mL for L. fermentum and P. fluorescens Migula, respectively. In addition, the shelf-life of the treated, raw, and uninoculated product was prolonged from 14 to 35 days, compared with standard pasteurization, to as long as 63 days with the LTST amendment. Sensory analysis of samples also demonstrated equal or greater preference for LTST + pasteurization treated milk when compared to pasteurization alone (α = 0.05). Conventional pasteurization was effective at reducing the above mentioned microorganisms by as much as 5.0 log10 cfu/mL. However, LTST was able to achieve 7.0–8.0 log10 cfu/mL reduction of the same microorganisms. In addition, BActerial Rapid Detection using Optical scattering Technology detected and identified microorganisms isolated both pre- and post-treatment, of which the only organisms surviving LTST were Bacillus spp. Increased lethality, improved shelf-life, and equal or better organoleptic characteristics without increased energy consumption demonstrate the effectiveness of the incorporation of LTST. The improved shelf-life may potentially have major impacts in the dairy industry in terms of shipping and overall sustainability.
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Affiliation(s)
- Phillip R Myer
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996 USA
| | - Kyle R Parker
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054 USA
| | - Andrew T Kanach
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054 USA
| | - Tengliang Zhu
- Department of Food Science, Purdue University, West Lafayette, IN 47907-2009 USA
| | - Mark T Morgan
- Food Science and Technology Department, University of Tennessee, Knoxville, TN 37996 USA
| | - Bruce M Applegate
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054 USA ; Department of Food Science, Purdue University, West Lafayette, IN 47907-2009 USA
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Virulence Gene-Associated Mutant Bacterial Colonies Generate Differentiating Two-Dimensional Laser Scatter Fingerprints. Appl Environ Microbiol 2016; 82:3256-3268. [PMID: 26994085 DOI: 10.1128/aem.04129-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In this study, we investigated whether a laser scatterometer designated BARDOT (bacterial rapid detection using optical scattering technology) could be used to directly screen colonies of Listeria monocytogenes, a model pathogen, with mutations in several known virulence genes, including the genes encoding Listeria adhesion protein (LAP; lap mutant), internalin A (ΔinlA strain), and an accessory secretory protein (ΔsecA2 strain). Here we show that the scatter patterns of lap mutant, ΔinlA, and ΔsecA2 colonies were markedly different from that of the wild type (WT), with >95% positive predictive values (PPVs), whereas for the complemented mutant strains, scatter patterns were restored to that of the WT. The scatter image library successfully distinguished the lap mutant and ΔinlA mutant strains from the WT in mixed-culture experiments, including a coinfection study using the Caco-2 cell line. Among the biophysical parameters examined, the colony height and optical density did not reveal any discernible differences between the mutant and WT strains. We also found that differential LAP expression in L. monocytogenes serotype 4b strains also affected the scatter patterns of the colonies. The results from this study suggest that BARDOT can be used to screen and enumerate mutant strains separately from the WT based on differential colony scatter patterns. IMPORTANCE In studies of microbial pathogenesis, virulence-encoding genes are routinely disrupted by deletion or insertion to create mutant strains. Screening of mutant strains is an arduous process involving plating on selective growth media, replica plating, colony hybridization, DNA isolation, and PCR or immunoassays. We applied a noninvasive laser scatterometer to differentiate mutant bacterial colonies from WT colonies based on forward optical scatter patterns. This study demonstrates that BARDOT can be used as a novel, label-free, real-time tool to aid researchers in screening virulence gene-associated mutant colonies during microbial pathogenesis, coinfection, and genetic manipulation studies.
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He Y, Reed S, Bhunia AK, Gehring A, Nguyen LH, Irwin PL. Rapid identification and classification of Campylobacter spp. using laser optical scattering technology. Food Microbiol 2015; 47:28-35. [DOI: 10.1016/j.fm.2014.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/10/2014] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
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18
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Rapid pathogen detection by lateral-flow immunochromatographic assay with gold nanoparticle-assisted enzyme signal amplification. Int J Food Microbiol 2015; 206:60-6. [PMID: 25955290 DOI: 10.1016/j.ijfoodmicro.2015.04.032] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/13/2015] [Accepted: 04/19/2015] [Indexed: 11/22/2022]
Abstract
To date most LF-ICA format for pathogen detection is based on generating color signals from gold nanoparticle (AuNP) tracers that are perceivable by naked eye but often these methods exhibit sensitivity lower than those associated with the conventional enzyme-based immunological methods or mandated by the regulatory guidelines. By developing AuNP avidin-biotin constructs in which a number of enzymes can be labeled we report on an enhanced LF-ICA system to detect pathogens at very low levels. With this approach we show that as low as 100 CFU/mL of Escherichia coli O157:H7 can be detected, indicating that the limit of detection can be increased by about 1000-fold due to our signal amplification approach. In addition, extensive cross-reactivity experiments were conducted (19 different organisms were used) to test and successfully validate the specificity of the assay. Semi-quantitative analysis can be performed using signal intensities which were correlated with the target pathogen concentrations for calibration by image processing.
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Bianco V, Marchesano V, Finizio A, Paturzo M, Ferraro P. Self-propelling bacteria mimic coherent light decorrelation. OPTICS EXPRESS 2015; 23:9388-9396. [PMID: 25968769 DOI: 10.1364/oe.23.009388] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We show here that live e-coli bacterial culture, thanks to the self-propelling feature, can significantly reduce the coherent noise. In fact, the typical self-propelled drive of such microorganisms provides enough time diversity in speckle patterns. Optical properties of a bacteria suspension have been investigated and analyzed thus showing that it behaves as a quite good optical speckle decorrelation device. Samples with different bacteria densities have been studied. The decorrelation effect has been demonstrated by probing the imaging performance in through transmission in coherent microscope configuration.
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20
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Tárnok A. Novel and improved cell recognition for diagnosis. Cytometry A 2014; 85:739-40. [PMID: 25139805 DOI: 10.1002/cyto.a.22522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/05/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Attila Tárnok
- Department of Pediatric Cardiology, Heart Centre Leipzig, University of Leipzig, Leipzig, Germany; Translational Centre for Regenerative Medicine (TRM), University of Leipzig, Leipzig, Germany
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21
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Tang Y, Kim H, Singh AK, Aroonnual A, Bae E, Rajwa B, Fratamico PM, Bhunia AK. Light scattering sensor for direct identification of colonies of Escherichia coli serogroups O26, O45, O103, O111, O121, O145 and O157. PLoS One 2014; 9:e105272. [PMID: 25136836 PMCID: PMC4138183 DOI: 10.1371/journal.pone.0105272] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/18/2014] [Indexed: 12/16/2022] Open
Abstract
Background Shiga-toxin producing Escherichia coli (STEC) have emerged as important foodborne pathogens, among which seven serogroups (O26, O45, O103, O111, O121, O145, O157) are most frequently implicated in human infection. The aim was to determine if a light scattering sensor can be used to rapidly identify the colonies of STEC serogroups on selective agar plates. Methodology/Principal Findings Initially, a total of 37 STEC strains representing seven serovars were grown on four different selective agar media, including sorbitol MacConkey (SMAC), Rainbow Agar O157, BBL CHROMagarO157, and R&F E. coli O157:H7, as well as nonselective Brain Heart Infusion agar. The colonies were scanned by an automated light scattering sensor, known as BARDOT (BActerial Rapid Detection using Optical scattering Technology), to acquire scatter patterns of STEC serogroups, and the scatter patterns were analyzed using an image classifier. Among all of the selective media tested, both SMAC and Rainbow provided the best differentiation results allowing multi-class classification of all serovars with an average accuracy of more than 90% after 10–12 h of growth, even though the colony appearance was indistinguishable at that early stage of growth. SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns. Colony scatter images were also tested with samples derived from pure and mixed cultures, as well as experimentally inoculated food samples. BARDOT accurately detected O157 and O26 serovars from a mixed culture and also from inoculated lettuce and ground beef (10-h broth enrichment +12-h on-plate incubation) in the presence of natural background microbiota in less than 24 h. Conclusions BARDOT could potentially be used as a screening tool during isolation of the most important STEC serovars on selective agar plates from food samples in less than 24 h.
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Affiliation(s)
- Yanjie Tang
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Huisung Kim
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Atul K. Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Amornrat Aroonnual
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
| | - Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
| | - Pina M. Fratamico
- USDA-ARS, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana, United States of America
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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Cho IH, Radadia AD, Farrokhzad K, Ximenes E, Bae E, Singh AK, Oliver H, Ladisch M, Bhunia A, Applegate B, Mauer L, Bashir R, Irudayaraj J. Nano/micro and spectroscopic approaches to food pathogen detection. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:65-88. [PMID: 24896312 DOI: 10.1146/annurev-anchem-071213-020249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Despite continuing research efforts, timely and simple pathogen detection with a high degree of sensitivity and specificity remains an elusive goal. Given the recent explosion of sensor technologies, significant strides have been made in addressing the various nuances of this important global challenge that affects not only the food industry but also human health. In this review, we provide a summary of the various ongoing efforts in pathogen detection and sample preparation in areas related to Fourier transform infrared and Raman spectroscopy, light scattering, phage display, micro/nanodevices, and nanoparticle biosensors. We also discuss the advantages and potential limitations of the detection methods and suggest next steps for further consideration.
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Affiliation(s)
- Il-Hoon Cho
- Bindley Bioscience and Birck Nanotechnology Center; Departments of
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Singh AK, Bettasso AM, Bae E, Rajwa B, Dundar MM, Forster MD, Liu L, Barrett B, Lovchik J, Robinson JP, Hirleman ED, Bhunia AK. Laser optical sensor, a label-free on-plate Salmonella enterica colony detection tool. mBio 2014; 5:e01019-13. [PMID: 24496794 PMCID: PMC3950520 DOI: 10.1128/mbio.01019-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 12/19/2013] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We investigated the application capabilities of a laser optical sensor, BARDOT (bacterial rapid detection using optical scatter technology) to generate differentiating scatter patterns for the 20 most frequently reported serovars of Salmonella enterica. Initially, the study tested the classification ability of BARDOT by using six Salmonella serovars grown on brain heart infusion, brilliant green, xylose lysine deoxycholate, and xylose lysine tergitol 4 (XLT4) agar plates. Highly accurate discrimination (95.9%) was obtained by using scatter signatures collected from colonies grown on XLT4. Further verification used a total of 36 serovars (the top 20 plus 16) comprising 123 strains with classification precision levels of 88 to 100%. The similarities between the optical phenotypes of strains analyzed by BARDOT were in general agreement with the genotypes analyzed by pulsed-field gel electrophoresis (PFGE). BARDOT was evaluated for the real-time detection and identification of Salmonella colonies grown from inoculated (1.2 × 10(2) CFU/30 g) peanut butter, chicken breast, and spinach or from naturally contaminated meat. After a sequential enrichment in buffered peptone water and modified Rappaport Vassiliadis broth for 4 h each, followed by growth on XLT4 (~16 h), BARDOT detected S. Typhimurium with 84% accuracy in 24 h, returning results comparable to those of the USDA Food Safety and Inspection Service method, which requires ~72 h. BARDOT also detected Salmonella (90 to 100% accuracy) in the presence of background microbiota from naturally contaminated meat, verified by 16S rRNA sequencing and PFGE. Prolonged residence (28 days) of Salmonella in peanut butter did not affect the bacterial ability to form colonies with consistent optical phenotypes. This study shows BARDOT's potential for nondestructive and high-throughput detection of Salmonella in food samples. IMPORTANCE High-throughput screening of food products for pathogens would have a significant impact on the reduction of food-borne hazards. A laser optical sensor was developed to screen pathogen colonies on an agar plate instantly without damaging the colonies; this method aids in early pathogen detection by the classical microbiological culture-based method. Here we demonstrate that this sensor was able to detect the 36 Salmonella serovars tested, including the top 20 serovars, and to identify isolates of the top 8 Salmonella serovars. Furthermore, it can detect Salmonella in food samples in the presence of background microbiota in 24 h, whereas the standard USDA Food Safety and Inspection Service method requires about 72 h.
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Affiliation(s)
- Atul K. Singh
- Department of Food Science, Molecular Food Microbiology Laboratory, Purdue University, West Lafayette, Indiana, USA
| | - Amanda M. Bettasso
- Department of Food Science, Molecular Food Microbiology Laboratory, Purdue University, West Lafayette, Indiana, USA
| | - Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, USA
| | - Murat M. Dundar
- Computer & Information Science Department, Indiana University, Purdue University at Indianapolis, Indianapolis, Indiana, USA
| | - Mark D. Forster
- Indiana State Department of Health, Indianapolis, Indiana, USA
| | - Lixia Liu
- Indiana State Department of Health, Indianapolis, Indiana, USA
| | - Brent Barrett
- Indiana State Department of Health, Indianapolis, Indiana, USA
| | - Judith Lovchik
- Indiana State Department of Health, Indianapolis, Indiana, USA
| | | | - E. Daniel Hirleman
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
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Pierzchalski A, Hebeisen M, Mittag A, Bocsi J, Di Berardino M, Tarnok A. Label-free hybridoma cell culture quality control by a chip-based impedance flow cytometer. LAB ON A CHIP 2012; 12:4533-4543. [PMID: 22907524 DOI: 10.1039/c2lc40408g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Impedance flow cytometry (IFC) was evaluated as a possible alternative to fluorescence-based methods for on-line quality monitoring of hybridoma cells. Hybridoma cells were cultured at different cell densities and viability was estimated by means of IFC and fluorescence-based flow cytometry (FCM). Cell death was determined by measuring the impedance phase value at high frequency in low conductivity buffer. IFC data correlate well with reference FCM measurements using AnnexinV and 7-AAD staining. Hybridoma cells growing at different densities in cell culture revealed a density-dependent subpopulation pattern. Living cells of high density cultures show reduced impedance amplitudes, indicating particular cellular changes. Dead cell subpopulations become evident in cultures with increasing cell densities. In addition, a novel intermediate subpopulation, which most probably represents apoptotic cells, was identified. These results emphasize the extraordinary sensitivity of high frequency impedance measurements and their suitability for hybridoma cell culture quality control.
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Ahmed WM, Bayraktar B, Bhunia A, Hirleman ED, Robinson JP, Rajwa B. Classification of bacterial contamination using image processing and distributed computing. IEEE J Biomed Health Inform 2012; 17:232-9. [PMID: 23060342 DOI: 10.1109/titb.2012.2222654] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Disease outbreaks due to contaminated food are a major concern not only for the food-processing industry but also for the public at large. Techniques for automated detection and classification of microorganisms can be a great help in preventing outbreaks and maintaining the safety of the nations food supply. Identification and classification of foodborne pathogens using colony scatter patterns is a promising new label-free technique that utilizes image-analysis and machine-learning tools. However, the feature-extraction tools employed for this approach are computationally complex, and choosing the right combination of scatter-related features requires extensive testing with different feature combinations. In the presented work we used computer clusters to speed up the feature-extraction process, which enables us to analyze the contribution of different scatter-based features to the overall classification accuracy. A set of 1000 scatter patterns representing ten different bacterial strains was used. Zernike and Chebyshev moments as well as Haralick texture features were computed from the available light-scatter patterns. The most promising features were first selected using Fishers discriminant analysis, and subsequently a support-vector-machine (SVM) classifier with a linear kernel was used. With extensive testing we were able to identify a small subset of features that produced the desired results in terms of classification accuracy and execution speed. The use of distributed computing for scatter-pattern analysis, feature extraction, and selection provides a feasible mechanism for large-scale deployment of a light scatter-based approach to bacterial classification.
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Bae E, Ying D, Kramer D, Patsekin V, Rajwa B, Holdman C, Sturgis J, Davisson VJ, Robinson JP. Portable bacterial identification system based on elastic light scatter patterns. J Biol Eng 2012; 6:12. [PMID: 22929757 PMCID: PMC3490744 DOI: 10.1186/1754-1611-6-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/23/2012] [Indexed: 11/21/2022] Open
Abstract
Background Conventional diagnosis and identification of bacteria requires shipment of samples to a laboratory for genetic and biochemical analysis. This process can take days and imposes significant delay to action in situations where timely intervention can save lives and reduce associated costs. To enable faster response to an outbreak, a low-cost, small-footprint, portable microbial-identification instrument using forward scatterometry has been developed. Results This device, weighing 9 lb and measuring 12 × 6 × 10.5 in., utilizes elastic light scatter (ELS) patterns to accurately capture bacterial colony characteristics and delivers the classification results via wireless access. The overall system consists of two CCD cameras, one rotational and one translational stage, and a 635-nm laser diode. Various software algorithms such as Hough transform, 2-D geometric moments, and the traveling salesman problem (TSP) have been implemented to provide colony count and circularity, centering process, and minimized travel time among colonies. Conclusions Experiments were conducted with four bacteria genera using pure and mixed plate and as proof of principle a field test was conducted in four different locations where the average classification rate ranged between 95 and 100%.
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Affiliation(s)
- Euiwon Bae
- Dr, J, Paul Robinson Purdue University Cytometry Laboratory, Bindley Bioscience Center, Purdue University, 1203 West State Street, Discovery Park, West Lafayette, IN, 47907, USA.
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Bae E, Patsekin V, Rajwa B, Bhunia AK, Holdman C, Davisson VJ, Hirleman ED, Robinson JP. Development of a microbial high-throughput screening instrument based on elastic light scatter patterns. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:044304. [PMID: 22559555 PMCID: PMC3339897 DOI: 10.1063/1.3697853] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/05/2012] [Indexed: 05/24/2023]
Abstract
A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.
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Affiliation(s)
- Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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Mialon M, Tang Y, Singh AK, Bae E, Bhunia AK. Effects of Preparation and Storage of Agar Media on the Sensitivity of Bacterial Forward Scattering Patterns. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojab.2012.13004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Arora P, Sindhu A, Dilbaghi N, Chaudhury A. Biosensors as innovative tools for the detection of food borne pathogens. Biosens Bioelectron 2011; 28:1-12. [DOI: 10.1016/j.bios.2011.06.002] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/04/2011] [Accepted: 06/07/2011] [Indexed: 11/25/2022]
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Tárnok A. Innovations in cytometry methods and technology. Cytometry A 2011; 79:241-2. [PMID: 21432989 DOI: 10.1002/cyto.a.21053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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