application of real-time pcr for detection of antibiotic resistant pathogens and shiga-toxin producing

226 Pages·2015·3.12 MB·English

by  Prashant Singh

APPLICATION OF REAL-TIME PCR FOR DETECTION
OF ANTIBIOTIC RESISTANT PATHOGENS AND
SHIGA-TOXIN PRODUCING ESCHERICHIA COLI

_______________________________________

A Dissertation
presented to
the Faculty of the Graduate School
at the University of Missouri-Columbia

_______________________________________________________

In Partial Fulfillment
of the Requirements for the Degree
Doctor of Philosophy

_____________________________________________________

By
PRASHANT SINGH
Dr. Azlin Mustapha, Dissertation Supervisor
May 2015
The undersigned, appointed by the dean of the Graduate School, have examined the
dissertation entitled

APPLICATION OF REAL-TIME PCR FOR DETECTION
OF ANTIBIOTIC RESISTANT PATHOGENS AND
SHIGA-TOXIN PRODUCING ESCHERICHIA COLI

presented by Prashant Singh,
a candidate for the degree of doctor of philosophy of Food Science, and hereby certify
that, in their opinion, it is worthy of acceptance.

Professor Azlin Mustapha, Food Science
Associate Professor Mengshi Lin, Food Science
Associate Adjunct Professor Guolu Zheng, Food Science
Professor Sheila Grant, Bioengineering
ACKNOWLEDGEMENTS

Every person that comes in our life has a role to play. When I look back, I
realized I have little bit of everyone who has touched my life and that little bit of
everyone constitutes me. I would like to express my sincere gratitude to PhD advisor
Prof. Azlin Mustapha who gave me this opportunity and taught me so many things.
I would like to thank Dr. Yvonne Pfeifer (Robert Koch Institute, Germany), Dr.
Katia Jaton-Ogay (Institute of Microbiology, Switzerland), Dr. Anette M. Hammerum
(Statens Serum Institut Microbiology & Infection Control, Denmark), Dr. Brian Johnston
(VA Medical Center, USA), Dr. Luxin Wang (Auburn University, USA), and Dr. T. G.
Nagaraja (Kansas State University, USA) for providing me DNA samples required for
my research. In addition to that I would also like to thank Dr. Victoria Vieira-Potter and
Dr. Kamlendra Singh for their friendship and support.
Special thanks to all my lab members for all your love and support. Finally I
would like to thank to all the staff members of Food Science Department and University
of Missouri.
Thank you all for your kindness, help, patience, generosity and compassion.

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TABLE OF CONTENTS
ACKNOWLEDGEMENTS......................................................................................................... ii
LIST OF FIGURES ................................................................................................................... vii
LIST OF TABLES ..................................................................................................................... ix
ABSTRACT ............................................................................................................................... xi
Chapter 1 Introduction..................................................................................................... 1
REFERENCES ............................................................................................................................ 4
Chapter 2 Literature Review ........................................................................................... 5
2.1 Antibiotic Resistance in Bacteria Associated with Food Animals ........................................ 5
2.2 The origin of antibiotic resistance ......................................................................................... 6
2.3 Antibiotic resistance in foodborne pathogens and reservoirs ................................................ 7
2.4 Beef Cattle and Associated Antibiotic Resistance ................................................................. 8
2.5 Poultry and Associated Antibiotic Resistance ....................................................................... 9
2.6 Salmonella ........................................................................................................................... 10
2.6.1 Multi-Drug Resistant Salmonella ............................................................................................... 11
2.7 Salmonella Isolation ............................................................................................................ 15
2.7.1 Real-Time PCR Detection of Salmonella ................................................................................. 16
2.7.2 Gene Targets for the PCR based Detection of Salmonella ................................................ 22
2.8 Carbapenems and Extended Spectrum beta-lactam Resistance in Enterobacteriaceae ....... 25
2.8.1 Extended spectrum beta lactamase .......................................................................................... 27
2.8.1.1 Types of ESBL ............................................................................................................................................... 29
2.8.2 Carbapenemase ................................................................................................................................. 33
2.8.2.1 Classification of carbapenemases ........................................................................................................ 36
2.8.2.2 Distribution of carbapenemase enzymes ......................................................................................... 39
2.8.3 Epidemiology and spread of these enzymes ......................................................................... 42
2.8.3.1 Primary Reservoir ...................................................................................................................................... 42
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2.8.3.2 Mobile Genetic Elements ......................................................................................................................... 42
2.8.3.3 Exchange among human population .................................................................................................. 43
2.8.4 Need for detection of antibiotic resistance............................................................................ 43
2.8.4.1 Need for molecular methods for antibiotic susceptibility testing ......................................... 45
2.8.4.2 Ideal gene targets for rapid detection of antibiotic resistant pathogens ........................... 46
2.8.4.3 PCR based method for ESBL and carbapenems detection ........................................................ 50
2.9 Shiga Toxin-Producing Escherichia Coli ............................................................................ 55
2.9.1 Foodborne non-O157 STEC outbreaks ................................................................................... 57
2.9.2 Virulence factors of STEC .............................................................................................................. 57
2.9.3 Methods for the detection of E. coli O157 and non-O157 STEC .................................... 59
2.9.3.1 Culture-based methods ............................................................................................................................ 59
2.9.3.2 Immunological methods .......................................................................................................................... 60
2.9.3.3 Nucleic acid amplification based assay ............................................................................................. 62
REFERENCES .......................................................................................................................... 66
Chapter 3 Multiplex TaqMan® Detection of Pathogenic and Multi-Drug Resistant
Salmonella ...................................................................................................... 83
3.1 INTRODUCTION ............................................................................................................... 84
3.2 MATERIAL AND METHODS ........................................................................................... 88
3.2.1 Bacterial strains ................................................................................................................................ 88
3.2.2 Phenotypic and genotypic determination of antibiotic resistance .............................. 88
3.2.3 Bacterial DNA isolation .................................................................................................................. 89
3.2.4 Primers and probes ......................................................................................................................... 89
3.2.5 Standardization of IAC concentration ..................................................................................... 90
3.2.7 Sensitivity of the real-time PCR assay ..................................................................................... 93
3.2.8 Preparation of artificially spiked samples ............................................................................. 94
3.3 RESULTS ............................................................................................................................ 96
3.3.1 Antibiotic resistance of tested Salmonella strains .............................................................. 96
3.3.2 Specificity of the assay ................................................................................................................... 98
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3.3.3 Sensitivity of the assay ................................................................................................................... 98
3.3.4 Detection of antibiotic resistant Salmonella in spiked samples................................. 100
3.4 DISCUSSION .................................................................................................................... 102
3.5 CONCLUSION ................................................................................................................. 107
REFERENCES ........................................................................................................................ 108
Chapter 4 Development of a real-time PCR melt curve assay for simultaneous
detection of virulent and antibiotic resistant Salmonella ........................ 111
4.1 INTRODUCTION ............................................................................................................. 112
4.2 MATERIAL AND METHODS ......................................................................................... 115
4.2.1 Bacterial strains ............................................................................................................................. 115
4.2.3 Bacterial DNA extraction............................................................................................................ 116
4.2.4 Primer design.................................................................................................................................. 116
4.2.5 Real-time PCR ................................................................................................................................. 119
4.2.6 Sensitivity of the real-time PCR assay .................................................................................. 119
4.2.7 Preparation of artificially spiked food samples ................................................................ 120
4.3 RESULTS .......................................................................................................................... 121
4.3.1 Antibiotic resistance of Salmonella strains ........................................................................ 121
4.3.2 Real-time PCR ................................................................................................................................. 126
4.3.3 Sensitivity of the assay ................................................................................................................ 129
4.3.4 Detection of antibiotic resistant Salmonella in spiked samples................................. 130
4.4 DISCUSSION .................................................................................................................... 134
4.5 CONCLUSIONS ............................................................................................................... 141
REFERENCES ........................................................................................................................ 142
Chapter 5 Multiplex real-time PCR assay for the Detection of Extended-Spectrum
β-Lactamases and Carbapenemase Producing Genes Using Melting
Curve Analysis ............................................................................................ 147
5.1 INTRODUCTION ............................................................................................................. 148
5.2 MATERIALS AND METHODS ...................................................................................... 151
5.2.1 Procurement of standard DNA sample and cultures ...................................................... 151
5.2.2 Bacterial DNA extraction............................................................................................................ 152
5.2.3 Primer design.................................................................................................................................. 152
5.2.4 Internal amplification control (IAC) design ....................................................................... 153
5.2.5 Real-time PCR ................................................................................................................................. 153
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5.2.6 Validation of the assay ................................................................................................................ 157
5.2.7 In silico analysis of primer pairs used for multiplex assay .......................................... 157
5.3 RESULTS .......................................................................................................................... 157
5.3.1 Multiplex real-time PCR ............................................................................................................. 157
5.3.2 Validation of the assay ................................................................................................................ 159
5.3.3 In silico analysis of primer pair used for multiplex assay ............................................ 162
5.4 DISCUSSION .................................................................................................................... 162
5.5 CONCLUSIONS ............................................................................................................... 168
REFERENCES ........................................................................................................................ 169
Chapter 6 Multiplex real-time PCR assays for the Detection of Eight Shiga Toxin-
Producing Escherichia coli Using Melting Curve Analysis ..................... 172
6.2 MATERIALS AND METHODS ...................................................................................... 175
6.2.1 Bacterial strains ............................................................................................................................. 175
6.2.2 Bacterial DNA extraction............................................................................................................ 177
6.2.3 Primer design.................................................................................................................................. 177
.......................................................................................................................................................................... 181
6.2.4 Development of real-time PCR melt curve assay ............................................................. 182
6.2.5 IAC design ......................................................................................................................................... 182
6.2.6 Real-time PCR ................................................................................................................................. 182
6.2.7 Limit of detection of the real-time PCR assay ................................................................... 183
6.2.8 Comparison of enrichment media .......................................................................................... 184
6.2.9 Preparation of artificially spiked food samples ................................................................ 184
6.3 RESULTS .......................................................................................................................... 187
6.3.1 Real-time PCR ................................................................................................................................. 187
6.3.2 Limit of detection of the assay ................................................................................................. 190
6.3.3 Comparison of enrichment media .......................................................................................... 191
6.3.4 Artificially spiked food samples .............................................................................................. 192
6.3.5 Spiked food sample according to USDA recommendation ........................................... 193
6.4 DISCUSSION .................................................................................................................... 195
6.5 CONCLUSIONS ............................................................................................................... 201
REFERENCES ........................................................................................................................ 202
Chapter 7 CONCLUSIONS AND FUTURE STUDIES ............................................ 206
VITA........................................................................................................................................ 211

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LIST OF FIGURES
Figure 2.1 Salmonella Typhimurium DT104 integron resistance gene cluster ................ 13
Figure 2.2 An overview of Salmonella isolation from food samples ............................... 15
Figure 2.3 Phylogenetic tree of the metallo-carbapenemase and serine carbapenemase
genes ............................................................................................................... 35
Figure 3.1 Standard curve constructed using serially diluted DNA99
Figure 3.2 Standard curve constructed using a spiked beef sample ............................... 100
Figure 4.1 Multiplex assay for the detection of virulent and antibiotic resistant
Salmonella..................................................................................................... 128
Figure 4.2 Sensitivity of multiplex assay: DNA concentrations ranging from 20 ng to
200 fg using MeltDoctor™ master mix ........................................................ 129
Figure 4.3 Standard curve constructed using serially diluted DNA ............................... 130
Figure 5.1 Multiplex assay for the detection of bla , bla , bla , bla and bla
VIM KPC CMY CTX NDM
with IAC........................................................................................................ 158
Figure 5.2: Multiplex assay for the detection of bla , bla , bla , bla and bla
OXA IMP ACC TEM SHV
with IAC........................................................................................................ 159
Figure 6.1 Multiplex real-time PCR melt curve assay without IAC. .............................. 188
Figure 6.2 Multiplex real-time PCR melt curve assay with IAC. ................................... 188
Figure 6.3 Multiplex real-time PCR assay for the detection of STEC and Salmonella. . 189
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Figure 6.4 Sensitivity of multiplex real-time PCR at different DNA concentration ...... 190
Figure 6.5 Melt curve real-time PCR using 325 g ground beef spiked with 8 STEC
serogroups after 6 h of enrichment ............................................................... 193
Figure 6.6 Melt curve real time PCR using 325 g ground beef spiked with seven STEC
serogroups and Salmonella after 8 h of enrichment. ..................................... 195

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LIST OF TABLES
Table 2.1 Selected real-time PCR assay for the detection of Salmonella ........................ 17
Table 2.2 Classification of β-lactamases enzymes ........................................................... 36
Table 2.3 List of most important antibiotic resistance trait and genes that molecular
methods should be able to detect for the identification of Extended-spectrum
cephalosporins and Carbapenems resistance in Enterobacteriaceae ............... 48
Table 2.4 Partial list of commercially available assays for detecting non-O157 Shiga
toxin–producing Escherichia coli ................................................................... 63
Table 3.1 Primers and probes for real-time PCR assays. .................................................. 92
Table 3.2 Phenotypic and genotypic antibiotic resistance profile of Salmonella isolates. 97
Table 3.3 Multiplex real-time PCR results of artificially contaminated food samples. . 101
Table 4.1 Primers used for real-time PCR melt curve assay. ......................................... 118
Table 4.2 Phenotypic and genotypic antibiotic resistance profile of Salmonella isolates.
....................................................................................................................... 123
Table 4.3 Melting temperature (T ) of the amplicons. ................................................... 127
m
Table 4.4 Multiplex real-time PCR results of artificially contaminated food samples. . 131
Table 4.5 Mean Ct values of each PCR primer in uniplex format, using ground beef of
different fat contents. .................................................................................... 133
Table 5.1 Primer set for the first multiplex assay. .......................................................... 155
Table 5.2 Primer set for the second multiplex assay. ..................................................... 156
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