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Shigatoxin Producing Escherichia Coli O157 and Non-O157 Serotypes in Producer-Distributor Bulk Milk

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Shigatoxin Producing Escherichia Coli O157 and Non-O157 Serotypes in Producer-Distributor Bulk Milk Shigatoxin producing Escherichia coli O157 and non-O157 serotypes in producer-distributor bulk milk By Victor Ntuli Submitted in partial fulfilment of the requirements for the degree Ph.D. (Food Science) In the Department of Food Science Faculty of Natural and Agricultural Sciences University of Pretoria Republic of South Africa June, 2017 DECLARATION I, Victor Ntuli declare that the thesis, which I hereby submit for the degree Ph.D. Food Science at the University of Pretoria, is my own work and has not previously been submitted by me for a degree at this or any other tertiary institution. June, 2017 i ABSTRACT Shigatoxin producing Escherichia coli O157 and non-O157 serotypes in producer- distributor bulk milk By Victor Ntuli Supervisor: Prof. E. M. Buys Co-supervisor: Dr. P. K. M. Njage Degree: Ph.D. Food Science Several recent large outbreaks of gastrointestinal diseases have highlighted the threat posed by morbidity and mortality associated with shigatoxin-producing Escherichia coli (STEC). Furthermore, the treatment of STEC infections is now threatened by the emergence of antibiotic resistance which is an alarming health concern in the world of medicine. The most implicated STEC in foodborne disease outbreaks across the globe is O157 serotype, although some emerging STEC non-O157 serotypes are increasingly becoming recognised as foodborne pathogens of important public health concern. This study was undertaken to characterise bacterial species in raw and pasteurised producer-distributor bulk milk (PDBM) with specific emphasis on E. coli and other Enterobacteriaceae. E. coli was further investigated for the prevalence and distribution of virulence factors (stx 1, stx 2 and hlyA), serotypes and antibiotic resistance patterns, which also ii included extended-spectrum β-lactamase (ESBL) producing capacity. Subsequently, the study further estimated the haemolytic uraemic syndrome (HUS) risk associated with the consumption of STEC contaminated PDBM and also estimated the resulting burden of illness that may be associated with the consumption of such milk in South Africa (SA). A total of 258 PDBM samples were collected, using convenience sampling, from outlets (purchase points) in eight different geographical provinces in SA. Isolation, detection and enumeration of total aerobic bacteria, coliforms and E. coli were carried out using 3M E. coli /coliform petrifilm plates. Matrix assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI- TOF-MS) was used for the rapid identification of the bacterial isolates. The identification of E. coli was confirmed using PCR of the uidA gene. Further characterisation of E. coli into serogroups, identification of virulence factors and antibiotic resistance profiles were then performed. E. coli O157 was characterised using selective media and confirmed using mismatch amplification mutation assay (MAMA)-multiplex PCR. Identification of E. coli -serogroups was carried out by the restriction of amplified O-antigen gene cluster (rfb-RFLP), coupled with serum agglutination assay. Virulence factors (stx 1, stx 2 and hlyA) were determined using both phenotypic and genotypic characterisation. Antimicrobial agent susceptibility tests and detection of extended spectrum beta-lactamase (ESBL) producing capacity of the E. coli isolates were performed using phenotypic characterisation. Finally, a quantitative risk assessment for STEC in PDBM was also conducted. More than 60% of the PDBM samples were found not to be fit for human consumption on the basis of the minimum standards prescribed in the Foodstuffs, Cosmetics and Disinfectants Act (Act 54 of 1972). Raw and pasteurised PDBM was contaminated with a wide diversity of Enterobacteriaceae species, which included spoilage microbiota. iii Multidrug resistant E. coli strains, as well as strains potentially capable of hydrolysing the 4th generation cephalosporins through producing extended spectrum β-lactamases were isolated from PDBM and this is a cause for concern as these strains are a potential source of antimicrobial resistant foodborne pathogens to humans through the food chain. Genotypic and phenotypic analysis of the E. coli confirmed that these strains are diverse, carry a variety of STEC virulence factor encoding genes associated with human diarrhoeal diseases and belong to O157 and non- O157 seropathotypes. However, the non-O157 STEC seropathotypes detected were not the serotypes implicated in foodborne illnesses in literature surveyed, mostly from Europe, Japan, Canada and the USA. Given that STEC contaminated PDBM may pose a significant public health threat to consumers, a quantitative microbial risk assessment was, therefore, performed. The assessment revealed that there was a higher risk of HUS cases per year for consumers of raw than pasteurised PDBM and also in age groups below 5 years. The risk is dependent on the variability surrounding the risk profile of the milk and is explicitly influenced by consumer behaviour. The study, therefore, recommends strict enforcement of and adherence to national standards, which regulate food hygiene in the dairy industry, especially for producers and suppliers of PDBM. Furthermore, the training on dairy technology and safety for producers and suppliers of PDBM by the relevant authorities need to be strengthened to improve public health and safety. The raising of awareness of the health risks associated with the consumption of raw milk for, particularly, consumers of raw PDBM, also needs to be scaled-up for them to make informed decisions when buying and consuming milk. The awareness will indirectly encourage consumers to buy certified raw milk. iv DEDICATION To God the Almighty, my wife, Maleseli Ntuli and my kids Gina, Leseli and Naleli v ACKNOWLEDGEMENTS It is very difficult, in the work of this kind, to render adequate thanks where thanks are due. I am very grateful to those who helped in the development of this thesis. A very big debt of gratitude is due to Professor Elna M. Buys, my supervisor and my co-supervisor, Dr. Patrick M. K Njage, who assisted me closely at every little stage of my work. May the Lord bless them abundantly. Special thanks go to Prof Andrea Serraino, and Dr Paolo Bonilauri from Italy who contributed significantly to the risk assessment chapter. Great imagination and generosity were shown by the Milk SA in funding the research project. I am indebted to the National Research Foundation (NRF) of South Africa, which awarded me a bursary for my Ph.D. studies and also provided grants to attend international conferences. My sincere thanks are due to the Department of Food Science technical staff, for their technical assistance. To my colleague, Desmond Mugadza, and the food microbiology team, thanks for being there, you created a workable environment for me. I would also like to extend my gratitude to Mr. Peter Chatanga for a constant source of encouragement and advice. I would like to appreciate my lovely wife (Maleseli Ntuli), my mother (Gladys Ntuli), my brothers and sisters for their support and encouragement during the course of this Ph.D. work. Last but not least, I would like to thank the Almighty God, because of his grace I was allowed to do my work. vi TABLE OF CONTENTS DECLARATION............................................................................................................................ i ABSTRACT ................................................................................................................................... ii DEDICATION............................................................................................................................... v ACKNOWLEDGEMENTS ........................................................................................................ vi TABLE OF CONTENTS ........................................................................................................... vii LIST OF TABLES ...................................................................................................................... xii LIST OF FIGURES ................................................................................................................... xiv CHAPTER ONE ........................................................................................................................... 1 GENERAL INTRODUCTION .................................................................................................... 1 CHAPTER TWO .......................................................................................................................... 5 LITERATURE REVIEW ............................................................................................................ 5 2.1. INTRODUCTION ................................................................................................................... 6 2.2. MILK AND DAIRY PRODUCTION ..................................................................................... 6 2.3. MILK PRODUCTION IN SOUTH AFRICA ......................................................................... 9 2.3.1. South African milk value chain ................................................................................... 12 2.3.1.1. Milk from the formal value chain ......................................................................... 12 2.3.1.2. Milk from the informal value chain ...................................................................... 14 2.3.2. Producer-distributor bulk milk (PDBM) ..................................................................... 15 2.3.2.1.
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