Optimization of Flow Cytometry Assays for the Detection of Injured Foodborne Pathogenic Bacteria

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Optimization of Flow Cytometry Assays for the Detection of Injured Foodborne Pathogenic Bacteria OPTIMIZATION OF FLOW CYTOMETRY ASSAYS FOR THE DETECTION OF INJURED FOODBORNE PATHOGENIC BACTERIA Alicia Subires Orenes Facultat de Veterinària Departament de Ciència Animal i dels Aliments Doctoral thesis OPTIMIZATION OF FLOW CYTOMETRY ASSAYS FOR THE DETECTION OF INJURED FOODBORNE PATHOGENIC BACTERIA Alicia Subires Orenes Bellaterra (Cerdanyola del Vallès), 2015 Josep Yuste Puigvert, professor agregat, i Marta Capellas Puig, professora titu- lar del Departament de Ciència Animal i dels Aliments de la Universitat Autò- noma de Barcelona, fan constar que la llicenciada en Ciència i Tecnologia dels Aliments Alicia Subi- res Orenes ha dut a terme, sota la seva direcció, el treball titulat “Optimization of flow cytometry assays for the detection of injured foodborne pathogenic bacteria”, que presenta per optar al grau de Doctor. I perquè així consti, signem el present document a Bellaterra (Cerdanyola del Vallès), el 27 de juliol de 2015. Josep Yuste Puigvert Marta Capellas Puig This project was supported by grant AGL2007-66877/ALI from the Spanish Ministry of Education and Science (MEC). Alicia Subires benefited from a grant by the Commission for Universities and Research of the Ministry of Innovation, Universities and Enterprise (DIUE) of the Autonomous Government of Catalo- nia. to find you in infinity of space and time one must first divide and then combine J. W. von Goethe Agraïments Als meus directors de tesi, la Marta i el Josep, dels qui he après tant durant aquests anys, per confiar en mi i en la meva capacitat per tirar la feina endavant, per la seva paciència i bons consells. A la Manuela Costa, tècnica del servei de citometria de la UAB, per la seva amabilitat en tot moment i per iniciar-me en la citometria de flux. I would like to acknowledge Dr. Tjakko Abee, who gave me the chance to work with his research group, and Dr. Maarten Mols, who gave me so many valuable lab tips. A Manuela Hernández, por acogerme en su despacho estos últimos meses de redac- ción, por su buen humor, y por enseñarme tanto durante las prácticas del “workshop”. A la resta de gent del Departament: becaris, tècnics, professors. Uns ja han marxat, altres encara hi són, però a tots els agraeixo la seva ajuda quan ho he necessitat, la seva amabilitat, el seu suport i els bons moments, tant dins com fora de la feina. Als meus pares i a la meva germana. Quina sort tenir-vos... Publications and presentations related to this thesis Publications Title: Flow cytometry immunodetection and membrane integrity assessment of Esch- erichia coli O157:H7 in ready-to-eat pasta salad during refrigerated storage Authors: A. Subires, J. Yuste, M. Capellas Reference: International Journal of Food Microbiology, 2014, 168-169: 47-56 Scientific communications Title: Immunodetection and membrane integrity assessment of Escherichia coli O157:H7 by three-colour flow cytometry Authors: A. Subires, J. Yuste, M. Capellas Meeting: 5th International Conference on Analysis of Microbial Cells at the Single Cell Level Place and date: Carry-Le-Rouet, France, 5-8 November, 2011 Type of communication: Poster communication Title: Assessment of green-fluorescent nucleic acid stains as bacterial viability indica- tors for flow cytometry analysis Authors: A. Subires, M. Capellas, S. De Lamo, J. Yuste Meeting: 22nd International Symposium of the International Committee on Food Microbiology and Hygiene, Food Micro 2010: Microbial behaviour in the food chain Place and date: Copenhagen, Denmark, 30 August-3 September, 2010 Type of communication: Poster communication Title: Inactivation-associated reactive oxygen species formation in heat- and acid- stressed bacteria Authors: A. Subires, M. Mols, M. Capellas, J. Yuste, T. Abee Meeting: 22nd International Symposium of the International Committee on Food Microbiology and Hygiene, Food Micro 2010: Microbial behavior in the food chain Place and date: Copenhagen, Denmark, 30 August-3 September, 2010 Type of communication: Oral communication Title: Flow cytometry for injured pathogen detection Authors: A. Subires, J. Yuste, M. Capellas Meeting: 30th Annual Rapid Methods and Automation in Microbiology Work- shop/Symposium Place and date: Manhattan, KS, USA, 11-18 June, 2010 Type of communication: Lecture Title: Flow cytometry detection of Escherichia coli O157:H7 stressed by chemical and physical treatments Authors: A. Subires, J. Yuste, M. Capellas Meeting: V European Symposium on Food Safety Place and date: Berlin, Germany, 7-9 October, 2009 Type of communication: Poster communication Contents i Table of contents Abstract .......................................................................................................... 1 Resumen ......................................................................................................... 3 Chapter 1. Literature review ........................................................................ 7 1. Injured bacteria in food .............................................................................................................. 9 1.1. Minimally processed food as pathogen vectors ..................................................... 9 1.2. Stress exposure throughout the food chain ......................................................... 10 1.2.1. Stress factors and cellular targets................................................................ 10 1.2.2. Stress adaptive responses .............................................................................. 13 1.3. Potential public health hazards posed by injured bacteria ............................ 15 2. Detection of injured cells ........................................................................................................ 16 2.1. Culture-based methods ................................................................................................ 17 2.1.1. Differential plating method ........................................................................... 17 2.1.2. Thin agar layer method ................................................................................... 18 2.2. Culture-independent methods .................................................................................. 19 2.2.1. Molecular methods ........................................................................................... 19 2.2.2. Fluorescence-based techniques .................................................................. 21 2.2.2.1. Assessment of physiological parameters by fluorescent probes ................................................................................................... 21 2.2.2.2. Fluorescence detection ................................................................. 34 3. Basic principles of flow cytometry ....................................................................................... 37 3.1. Instrumentation ............................................................................................................... 38 3.1.1. Fluidics ................................................................................................................... 38 3.1.2. Optics ..................................................................................................................... 40 3.1.2.1. Excitation optics................................................................................ 40 3.1.2.2. Collection optics ............................................................................... 42 3.1.3. Signal processing electronics ....................................................................... 43 3.1.3.1. Analog signal processing .............................................................. 43 3.1.3.2. Digital signal processing ............................................................... 46 3.2. Data display and analysis ............................................................................................. 46 ii Contents 3.3. Cell parameters measured by flow cytometry ..................................................... 48 3.3.1. Scattering signals ............................................................................................... 48 3.3.2. Fluorescence signals......................................................................................... 50 3.4. Flow cytometers for bacterial analysis .................................................................... 53 4. Flow cytometry measurements of food-related bacteria .......................................... 55 4.1. Challenges of flow cytometry detection of bacteria in food .......................... 55 4.2. Sample preparation ........................................................................................................ 56 4.2.1. Liquid foods ......................................................................................................... 59 4.2.2. Semi-solid and solid foods ............................................................................. 60 4.3. Applications ....................................................................................................................... 60 4.3.1. Identification of bacteria ................................................................................. 60 4.3.2. Enumeration of bacteria ................................................................................. 69 4.3.3. Physiological state assessment .................................................................... 72 5. References..................................................................................................................................... 74 Chapter 2. Introduction
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