PHYSICO-CHEMICAL AND BACTERIOLOGICAL QUALITY OF WATER, AND ANTIMICROBIAL SUSCEPTIBILITY OF PATHOGENIC ISOLATES FROM SELECTED WATER SOURCES IN SAMBURU SOUTH. BY JEOPHITA JUNE MWAJUMA (B.Sc, P.G.D.E) REG. NO. I56/7341/02 DEPARTMENT OF PLANT AND MICROBIAL SCIENCES A thesis submitted in partial fulfillment of the requirements for the award of the degree of Master of Science (Microbiology) in the School of Pure and Applied Sciences, Kenyatta University April 2010 ii DECLARATION I, Jeophita June Mwajuma, declare that this thesis is my original work and has not been presented for the award of a degree in any other University or any other award. Signature…………………………………... Date………………………….. We confirm that the work reported in this thesis was carried out by the candidate under our supervision. SUPERVISORS: Prof. Paul Okemo Department of Plant and Microbial Sciences Kenyatta University Signature…………………………………... Date………………………….. Dr. Alexander Njue Department of Plant and Microbial Sciences Kenyatta University Signature…………………………………... Date………………………….. Prof. Kiplagat Kotut Department of Plant and Microbial Sciences Kenyatta University Signature…………………………………... Date………………………….. iii DEDICATION For my girls, Neema and Wema. Babies, the sky is the limit! iv Formatted: Centered, Indent: Left: 0.25", 1. ACKNOWLEDGEMENT No bullets or numbering I wish to thank my supervisors Prof. Paul Okemo, Dr. Alexander Njue and Prof. Kiplagat Kotut for their expert advice and encouragement throughout the period of this study. My gratitude also goes to Earthwatch Institute for funding my research work through the Samburu Communities, Water and Wildlife project. I also wish to thank KEMRI, Welcome Trust Laboratories Kilifi, Wamba Mission Hospital and Mombasa Polytechnic University College for providing me with laboratory space and analytical tools. My sincere appreciation to Dr. Nicolas Oguge, Dr. Ben Munyali, Dr. Tom Achia, Mr. Philip Leitore, Ms. Jacinta Patrine, Mr. Lewa Pole, Mr. Ben Mvera, Mr.Humphrey Kisembe and Mr. John Kahindo for their individual professional assistance in the course of my research work. I thank my family, Steve, Baraka and Rani, for their warmth and support. v TABLE OF CONTENTS Page DECLARATION................................................................................................................ ii DEDICATION.................................................................................................................. iii ACKNOWLEDGEMENT ................................................................................................ iv TABLE OF CONTENTS……………………………………………………………….v LIST OF TABLES ......................................................................................................... viii LIST OF FIGURES .......................................................................................................... ix LIST OF PLATES………………………………………………………………………xi LIST OF ABBREVIATIONS AND ACRONYMS ....................................................... xii ABSTRACT .................................................................................................................... xiii CHAPTER ONE ................................................................................................................ 1 INTRODUCTION.............................................................................................................. 1 1.1 Background to the study .......................................................................................... 1 1.3 Research hypotheses ................................................................................................ 5 1.4 Research questions ................................................................................................... 5 1.5 The general objective ............................................................................................... 6 1.6 Specific objectives ................................................................................................... 6 CHAPTER TWO ............................................................................................................... 8 LITERATURE REVIEW ................................................................................................. 8 2.1 Biological hazards of water pollution ...................................................................... 8 2.2 Transmission of enteropathogens .......................................................................... 10 2.3 Bacteriological indicators of pollution ................................................................... 11 2.3.1 Concept of indicator organisms ..................................................................... 11 2.3.2 Total coliforms ............................................................................................... 14 2.3.3 Faecal coliforms ............................................................................................. 16 2.3.4 Escherichia coli ............................................................................................. 16 2.4 Nuisance organisms ............................................................................................... 18 2.5 Pathogenic bacteria ................................................................................................ 19 2.5.1 Salmonella...................................................................................................... 19 2.5.2 Shigella .......................................................................................................... 21 2.5.3 Escherichia coli ............................................................................................. 22 2.5.4 Campylobacter ............................................................................................... 23 2.5.5 Vibrio ............................................................................................................. 24 vi 2.5.6 Leptospira ...................................................................................................... 24 2.5.7 Legionella ...................................................................................................... 25 2.5.8 Yersinia .......................................................................................................... 25 2.5.9 Aeromonas ..................................................................................................... 26 2.6 Antimicrobial sensitivity of common enteropathogens ......................................... 27 CHAPTER THREE ......................................................................................................... 29 MATERIALS AND METHODS .................................................................................... 29 3.1 Study area............................................................................................................... 29 3.1.1 Location ......................................................................................................... 29 3.1.2 Climate ........................................................................................................... 30 3.1.3 The People. .................................................................................................... 31 3.3 Field tests ............................................................................................................... 33 3.4 Bioassay ................................................................................................................. 34 3.4.1 Total plate count ............................................................................................ 34 3.4.2 Coliform tests ................................................................................................. 34 3.4.4 Test for Escherichia coli ................................................................................ 35 3.4.5 Biochemical tests ........................................................................................... 35 3.4.6 Faecal Streptococci ........................................................................................ 37 3.5 Isolation of bacterial pathogens ............................................................................. 37 3.5.1 Identification of Salmonella and Shigella ...................................................... 38 3.5.2 Detection of vibrios and aeromonads ............................................................ 38 3.5.3 Detection of Campylobacter jejuni ................................................................ 39 3.6 Antibiotic sensitivity testing .................................................................................. 39 3.6.1 Kirby-Bauer disc-diffusion method ............................................................... 39 3.6.2 Minimum inhibitory concentrations E- test ................................................... 40 3.7 Pulsed-field gel electrophoresis (PFGE) ................................................................ 41 3.8 Analysis of results .................................................................................................. 42 CHAPTER FOUR ............................................................................................................ 43 RESULTS ......................................................................................................................... 43 4.1 Physico-chemical properties of water in Samburu district .................................... 43 4.2 Bacterial quality of water ......................................................................................