HYPERSPECTRAL MICROSCOPY FOR EARLY AND RAPID DETECTION OF SALMONELLA SEROTYPES by MATTHEW BRENT EADY (Under the Direction of Bosoon Park) ABSTRACT Optical microbial detection methodologies have shown the potential as early and rapid pathogen detection methods. This proof-of-concept project explores the use of hyperspectral microscopy as a potential method for early and rapid classification of five Salmonella serotypes. Darkfield hyperspectral microscope images were collected at early incubation times of 6, 8, 10, and 12 hrs., then compared to 24 hrs. incubation. Hypercube data collected from cells were analyzed through multivariate data analysis (MVDA) methods to assess classification ability of early incubation times. A separate experiment was conducted to explore the ability of analyzing hyperspectral data collected from only informative spectral bands as opposed to the original 89 spectral bands. MVDA showed that incubation times as early as 8 hours had near identical spectra and classification abilities compared to 24 hours; while the original 89-point spectrum could be reduced to 3 selected spectral bands and maintain high serotype classification accuracy. INDEX WORDS: Salmonella, hyperspectral microscopy, early detection, rapid detection, multivariate data HYPERSPECTRAL MICROSCOPY FOR EARLY AND RAPID DETECTION OF SALMONELLA SEROTYPES by MATTHEW BRENT EADY BSA, The University of Georgia, 2011 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2014 © 2014 Matthew Brent Eady All Rights Reserved HYPERSPECTRAL MICROSCOPY FOR EARLY AND RAPID DETECTION OF SALMONELLA SEROTYPES by MATTHEW BRENT EADY Major Professor: Bosoon Park Committee: Mark Harrison Fanbin Kong Electronic Version Approved: Julie Coffield Interim Dean of the Graduate School The University of Georgia December 2014 iv DEDICATION To my wife and children: I dedicate this body of work in memory of my daughter, Amelie Eady, whose short time here taught me the true meaning of the word determination and inspired me to pursue the field of food safety, to my son, Judah Eady, who at the end of the day reminds me what all the effort is for, and finally, to my wife, Audrey Blackwell Eady, for her unshakable support of my education through the best of times, the worst of times, and everything in-between. v ACKNOWLEDGEMENTS I would like to thank my major professor, Dr. Bosoon Park, for the opportunity to be a part of his lab and his commitment to this project. I would also like to acknowledge my committee members, Drs. Mark Harrison and Fanbin Kong, for their time and input. I am grateful to Dr. Nasreen Bano for her expertise in microscopy and microbiological techniques. Thank you to Dr. Darlene Samuel for giving me my start with the USDA- ARS and the confidence to pursue this endeavor, and I am also grateful to Dr. Brian Bowker for his advice on the scientific writing and the peer review processes. The past few years would not be possible without the support and encouragement of my wife, Audrey Blackwell Eady. Her constant support and sacrifices over the past few years have made this body of work possible. I would also like to thank my mother, Elizabeth Eady, and brother, Jake Eady, for their encouragement and support. Also acknowledged are Brenda and Larry Blackwell for making the many trips to Athens, GA over the years to ease the stress-filled days. Sincerest appreciation, Mathew Eady vi TABLE OF CONTENTS Page ACKNOWLEDGEMENTS .................................................................................................v LIST OF TABLES ............................................................................................................. ix LIST OF FIGURES .............................................................................................................x CHAPTER 1 INTRODUCTION .............................................................................................1 References ....................................................................................................6 Figure .........................................................................................................10 2 LITERATURE REVIEW ................................................................................11 Optical detection of bacteria ......................................................................11 Hyperspectral imaging (HSI) and the hypercube.......................................13 Food quality applications of HSI ...............................................................14 Food safety applications of HSI .................................................................14 Hyperspectral microscope imaging (HMI) ................................................15 Data preprocessing methods ......................................................................16 HSI and chemometrics ...............................................................................17 Informative spectral band selection ...........................................................20 References ..................................................................................................21 Table ..........................................................................................................28 vii 3 RAPID AND EARLY DETECTION OF SALMONELLA SEROTYPES WITH HYPERSPECTRAL MICROSCOPE AND MULTIVARIATE DATA ANALYSIS ............................................................................................................29 Abstract ......................................................................................................30 Introduction ................................................................................................31 Materials and methods ...............................................................................33 Results ........................................................................................................38 Discussion ..................................................................................................40 References ..................................................................................................44 Figures and Tables .....................................................................................49 4 VISIBLE NEAR-INFRARED HYPERSPECTRAL MICROSCOPY AND INFORMATIVE BAND SELECTION FOR CLASSIFICATION OF SALMONELLA ENTERICA SEROTYPES......................................................55 Abstract ......................................................................................................56 Introduction ................................................................................................57 Materials and methods ...............................................................................60 Results ........................................................................................................66 Discussion ..................................................................................................67 References ..................................................................................................70 Figures and Tables .....................................................................................75 5 CONCLUSIONS..............................................................................................82 6 APPENDICES .................................................................................................85 viii A Principal component analyses score plots from reduced variable selection sets..............................................................................................................85 ix LIST OF TABLES Page Table 2.1: Overview of HIS methods applied to food for quality and safety assessment .28 Table 3.1: Difference of serotype values from a one-way ANOVA Fisher test, to compare relative average spectral peak ratios (590 nm / 538 nm) at incubation times of 8 - 24 hrs……. .............................................................................................................52 Table 3.2: Mahalanobis distance (MD) values between serotype clusters calculated from PCA score plots at incubation times of 8 - 24 hrs ..................................................53 Table 3.3: Soft-independent modeling of class analogy (SIMCA) for all serotypes within each incubation period ...........................................................................................54 Table 4.1: Description of variable sets selected for analyses ............................................80 Table 4.2: Confusion matrix results obtained from support vector machine classification (SVMC)..................................................................................................................81 x LIST OF FIGURES Page Figure 1.1: The hyperspectral microscope setup ...............................................................10 Figure 3.1: Hyperspectral microscope images of S. Typhimurium cells at different incubation times: (a) 6 hrs., (b) 8 hrs., (c) 10 hrs., (d) 12 hrs., and (e) 24 hrs. ......49 Figure 3.2: (a) Average spectra for S. Enteritidis normalized to 546nm, (b) average S. Enteritidis spectra with pretreatment algorithm applied ........................................50 Figure 3.3: PCA score plots with loading vectors for four incubation times: (a) 8 hrs., (b) 10 hrs., (c) 12 hrs., and (d) 24 hrs ..........................................................................51 Figure 4.1: Sample collection