MALDI-TOF-MS CHARACTERISATION OF ESCHERICHIA COLI ISOLATED FROM ROOF HARVESTED RAINWATER

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GENERAL INTRODUCTION

Globally, water is a scarce resource and an estimated 41 per cent of the world‘s population (or 2.3 billion people), live under ‗water stress‘, while 1.1billion people live without access to safe drinking water (FitzMauriCe, 2007). Access to clean water is worst in developing countries with at least one third of the population living without access to safe drinking water and about 1.87 million children die annually due to diarrhoea (Boschi-Pinto et al., 2008). In South Africa, the demand for water is in excess of natural water availability in several river basins, making it a water scarce country (Oberholster and Ashton, 2008; van Vuuren, 2008; Roux et al., 2010).
The country has different climates with variable rainfall patterns and high evaporation rates (Kahinda et al., 2009; Stockholm Environment Institute (SEI), 2009; Everson et al., 2011). Much of South Africa has predominantly hard rock geology, which limits groundwater availability. Hence, surface water is the most significant resource (van der Merwe-Botha, 2009). However, surface water has become very contaminated due to mining, industrial and agricultural activities and informal settlements next to riverbanks. Hence there is a need to evaluate other alternative sources of clean freshwater (Roux et al., 2010).
Social and demographic factors also contribute to water scarcity. One of these factors, for instance, is the distribution of significant settlements and industry that is determined by mineral deposits rather than water resources. In areas where groundwater is available, it is frequently over-exploited (van der Merwe-Botha, 2009). Worse still, population and economic growth in South Africa has resulted in increased demand on freshwater resources, including groundwater, man-made lakes and rivers (Ochse, 2007; Oberholster and Ashton, 2008; Kahinda et al., 2010; Viljoen et al., 2012). The quality of water from these resources has declined significantly due to pollution from urbanisation, agriculture, industries, mining and power generation (Department of Water Affairs and Forestry, 2002; Ochse, 2007; Roux et al., 2010).
Given the current patterns of water use and discharge, anticipated future population growth rates and expected socio-economic development trends, it is most likely that the available water resources will not be sufficient for future needs (Dalvie et al., 2003; Oberholster and Ashton, 2008; van der Merwe-Botha, 2009; Roux et al., 2010). It has been forecasted that freshwater resources in South Africa will be depleted and unable to meet the needs of industry and the people by the year 2030 (Postel, 2000; Turton, 2003). In as much, as the South African government has made great strides in the provision of clean domestic water, many poor and vulnerable South African inhabitants either have access to insufficient water or the available water is not of suitable quality for drinking or personal hygiene (Statistics South Africa, 2010).
The problems of inadequate supplies and insufficient treatment encourage searching for decentralised alternative approaches to access clean domestic and agricultural water, keeping in mind the technical and financial limitations of the poor living in under-developed areas (Alcock and Verste, 1987; Kahinda et al., 2007, 2010; Bulcock and Schulze, 2011; Kahinda and Taigbenu, 2011). Domestic rainwater harvesting (DRWH) describes the small-scale concentration, collection, storage, and use of rainwater runoff for production purposes. Roof rainwater harvesting (RRWH) is one of the broad categories of DRWH where water is collected from roofs, and stored in underground tanks (UGTs) or above-ground tanks (AGTs) and used for domestic purposes, including small scale production activities such as garden watering (Kahinda et al., 2007, 2010). Roof rainwater harvesting is one of the most appropriate alternative sources of potable and non-potable water supplies at household or community level as the world faces decreasing water sources and increasing energy crisis (Amin and Han, 2009).
Roof rainwater harvesting is an ancient technique for collecting and storing rainwater during the rainy season for later use. The practice of rainwater harvesting is verified by archaeological evidence which date back as far as 4000 years ago (Richards, 1989). Rainwater Harvesting (RWH) is not a conservation technique but rather a new water supply (Critchley and Siegert, 1991). Now that people are faced with decreasing water sources and increasing energy crisis, roof harvested rainwater RRWH may represent an alternative water source for supplying freshwater at household or community level (Houston and Still, 2002; Baiphethi et al., 2010; Stimie et al., 2010; Bulcock and Schulze, 2011; Botha et al., 2012; Viljoen et al., 2012). Roof rainwater harvesting has received increased attention worldwide as an alternative source of potable and non-potable water supplies. Potential applications of RRWH do exist for roof catchments in areas where a centralised water supply and distribution system are not adequate, and such applications are increasing (Han and Mun, 2007, 2011).

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TABLE OF CONTENTS :

  • DECLARATION
  • ACKNOWLEDGEMENTS
  • DEDICATION
  • RESUME
  • LIST OF FIGURES
  • LIST OF TABLES
  • TABLE OF ABBREVIATIONS
  • CHAPTER ONE GENERAL INTRODUCTION
    • References
  • CHAPTER TWO REVIEW OF THE STATE OF RAINWATER HARVESTING IN SOUTH AFRICAN RURAL COMMUNITIES
    • Abstract
    • 2.1 Introduction
    • 2.2 Rainwater harvesting
    • 2.3 Rainwater harvesting systems
    • 2.3.1 Catchment surface
    • 2.3.2 Gutters
    • 2.3.3 First flush diverters
    • 2.3.4 Storage tanks
    • 2.4 The acceptability of rainwater harvesting
    • 2.5 Legal aspects of rainwater harvesting
    • 2.6 The potential impact of rainwater harvesting on water related diseases
    • 2.7 Roof harvested rainwater quality
    • 2.8 Conclusion and recommendations
    • 2.9 References
  • CHAPTER THREE STRATEGY TOWARDS THE DEVELOPMENT OF RAINWATER HARVESTING RISK ASSESSMENT AND QUALITY GUIDELINES
    • Abstract
    • 3.1 Introduction
    • 3.2 The need for risk assessment criteria and guidance information
    • 3.3 Microbial risk assessment of roof harvested rainwater
    • 3.4 Systems approach: identifying potential hazards and health risks
    • 3.4.1 Microbial contaminants
    • 3.4.2 Zoonosis
    • 3.5 Quantitative microbial risk assessment
    • 3.5.1 Detection of pathogens in water
    • 3.5.2 Biofilm formation in rainwater storage tanks
    • 3.6 Discussion
    • 3.7 Conclusion and Recommendations
    • 3.8 References
  • CHAPTER FOUR A SCOPING STUDY ON PREVALENCE OF ESCHERICHIA COLI AND ENTeROCOCCUS SPECIES IN HARVESTED RAINWATER STORED IN TANKS
    • Abstract
    • 4.1 Introduction
    • 4.2 Methodology
    • 4.2.1 Sampling sites description and sample collection
    • 4.2.2 Microbiological analysis of water samples
    • 4.2.3 Faecal sample collection
    • 4.2.4 Recovery of isolates and presumptive identification
    • 4.2.5 Matrix-assisted laser desorption ionisation time of flight mass spectroscopy identification and characterisation of bacterial isolates
    • 4.2.6 Statistical Analysis
    • 4.3 Results
    • 4.3.1 Samples from Gauteng Province (Johannesburg and Pretoria)
    • 4.3.2 Prevalence of Escherichia coli, enterococci and Pseudomonas spp.in roof harvested rainwater samples from Luthengele village, Eastern Cape
    • 4.3.3 Prevalence of enterococci in roof harvested rainwater and bird faecal samples
    • 4.4 Discussion
    • 4.4.1 Factors affecting rainwater quality
    • 4.4.2 Rainwater quality from different technological and environmental settings
    • 4.4.3 Roof harvested rainwater quality
    • 4.4.4 Indicator bacteria in roof harvested rainwater
    • 4.4.5 Enterococci in roof harvested rainwater
    • 4.5 Conclusions and recommendations
    • 4.6 References
  • CHAPTER FIVE MALDI-TOF-MS CHARACTERISATION OF ESCHERICHIA COLI ISOLATED FROM ROOF HARVESTED RAINWATER
    • Abstract
    • 5.1 Introduction
    • 5.2 Methodology
    • 5.2.1 The Matrix-assisted laser desorption ionisation time of flight mass spectroscopy and characterisation of bacterial isolates were described in Chapter
      • 5.2.2 Polymerase chain reaction for detection of UidA gene in Escherichia coli
      • 5.2.3 Data evaluation
      • 5.3 Results
      • 5.3.1 Optimisation of experimental parameters
      • 5.3.2 Reproducibility of the MALDI-TOF-MS approach
      • 5.3.3 Study work flow
      • 5.3.4 MALDI-TOF-MS hierarchical cluster analysis of Escherichia coli isolates
      • 5.3.5 Strain groups similarity evaluation
      • 5.3.6 Machine learning
      • 5.3.7 Classification of Escherichia coli strains by their sources
      • 5.3.8 Principal component analysis
      • 5.4 Discussion
      • 5.4.1 Principal component analysis
      • 5.4.2 Support vector machine
      • 5.4.3 Comparison of MALDI-TOF-MS analysis and REP PCR analysis
      • 5.5 Conclusion
      • 5.6 References
  • CHAPTER SIX  ANTIBIOTIC RESISTANCE IN ESCHERICHIACOLI ISOLATES FROM ROOF HARVESTED RAINWATER (RHRW) TANKS
    • Abstract
    • 6.1 Introduction
    • 6.2 Methodology
    • 6.2.1 Area of the study and collection of samples
    • 6.2.2 Sample collection and isolation of presumptive Escherichia coli strains
    • 6.2.3 Faecal sample collection
    • 6.2.4 Recovery
    • 6.2.5 MALDI-TOF-MS identification and characterisation of bacterial isolates
    • 6.2.6 Polymerase chain reaction for detection of UidA gene in Escherichia coli
    • 6.2.7 Antimicrobial susceptibility testing
    • 6.2.8 Statistical analysis
    • 6.3 Results
    • 6.3.1 Antibiotic susceptibility
    • 6.3.2 Non-parametric test
    • 6.3.3 Correlation test
    • 6.3.4 Antibiotic resistance phenotypes
    • 6.3.5 Cluster analysis
    • 6.4 Discussion
    • 6.4.1 Antibiotic resistance profiles of samples
    • 6.4.2 Multiple antibiotic resistance patterns
    • 6.4.3 Cluster analysis of antibiotic resistance profiles
    • 6.5 Conclusion and recommendations for further studies
    • 6.6 References
  • CHAPTER SEVEN  PYROSEQUENCING ANALYSIS OF ROOF HARVESTED RAINWATER AND RIVER WATER USED FOR DOMESTIC PURPOSES IN LUTHENGELE VILLAGE IN THE EASTERN CAPE PROVINCE IN SOUTH AFRICA
    • Abstract
    • 7.1 Introduction
    • 7.2 Methodology
    • 7.2.2 DNA extraction and Pyrosequencing
    • 7.2.3 Pyrosequencing data processing and analysis
    • 7.2.4 Pathogen identification
    • 7.3 Results
    • 7.3.1 Sequencing depth
    • 7.3.2 Alpha diversity
    • 7.3.3 Phylum level diversity
    • 7.3.4 Class leveldiversity
    • 7.3.5 Diversity at order level
    • 7.3.6 Diversity at family level
    • 7.4 Cluster analysis and genus level diversity
    • 7.4.1 Cluster analysis
    • 7.4.2 Genus level diversity
    • 7.4.3 UniFrac analysis
    • 7.4.4 Detection of pathogenic signatures
    • 7.5 Discussion
    • 7.5.1 Microbial diversity
    • 7.5.2 Enviromental influence on microbial diversity
    • 7.5.3 Bacterial diversity
    • 7.5.4 Detection of pathogenic signatures
    • 7.6 Conclusion and recommendations
    • 7.7 References
  • CHAPTER EIGHT GENERAL DISCUSSION
    • References

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Microbial Quality of Rainwater Harvested from Rooftops, for Domestic use and Homestead Food Gardens

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