i OCCURRENCE OF RECTAL GONORRHOEA AND CHLAMYDIA AND ANTIBIOTIC SUSCEPTIBILITY PROFILE AMONG MEN WHO HAVE SEX WITH MEN AT THE KENYAN COAST CAROLINE JUMWA NGETSA (BSC) P150/CE/25905/2014 A RESEARCH THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE AWARD OF THE DEGREE OF MASTER OF SCIENCE (INFECTIOUS DISEASES) IN THE SCHOOL OF MEDICINE OF KENYATTA UNIVERSITY OCTOBER, 2018 ii DECLARATION iii DEDICATION I dedicate this work to my family; loving husband Oscar, wonderful sons Lloyd and Hans and my lovely daughter Stacey. For your patience and love during this worthy course, God bless you! iv ACKNOWLEDGEMENT Firstly, I would like to thank God for his goodness and mercy in granting me the strength to finish this worthy course in my life. I am deeply indebted to my supervisors Dr. Margaret Muturi and Dr. Nelson Menza both of Department of Medical Laboratory Sciences, Kenyatta University, without their guidance, support, good nature and patience I would not have made it this far. The doors to their offices remained open all the times when I had trouble with this write up. My gratitude also goes to my mentor and project director, Prof. E. Sanders for his guidance, encouragement and recommendation to applying for the International Aids Vaccine Initiative (IAVI) Advance Degree Support scholarship. My special gratitude also goes to the IAVI for funding the project that culminated in to this thesis. To my colleagues; Peter Mugo, Amin Hassan and Simon Chengo, Eunice Nduati, Ian Oyaro and all IAVI project Kilifi staff big thank you for helping me in this write up and putting things into perspective in this world of science writing. My special gratitude goes to my laboratory colleagues John Mwambi, Clara Karani, Benedict Chengo and all Bacto staff in Microbiology department in helping with the hard and laborious laboratory work and tolerating my many times away from the laboratory. Finally, to my husband Oscar and kids your awesomeness in putting up with me during this very important time of my life. May Almighty God bless you all abundantly! v TABLE OF CONTENTS Title Page DECLARATION .......................................................................................................... ii DEDICATION ............................................................................................................. iii ACKNOWLEDGEMENT ........................................................................................... iv TABLE OF CONTENTS ...............................................................................................v LIST OF TABLES ..................................................................................................... viii LIST OF FIGURES ..................................................................................................... ix LIST OF APPENDICES ................................................................................................x ABBREVIATIONS AND ACRONYMS .................................................................... xi ABSTRACT ................................................................................................................ xii 1.0 INTRODUCTION..................................................................................................1 1.1 Background information .......................................................................................... 1 1.2 Problem Statement ................................................................................................... 2 1.3 Justification .............................................................................................................. 3 1.4 Research Questions .................................................................................................. 3 1.5 Objectives of Study .................................................................................................. 4 1.5.1 General Objective ................................................................................................. 4 1.5.2 Specific Objectives ............................................................................................... 4 1.6 Significance of the Study ......................................................................................... 5 2.0 LITERATURE REVIEW .....................................................................................6 2.1 Sexually Transmitted Infections .............................................................................. 6 2.2 Sexual Transmitted Infections among men who have sex with men ....................... 6 2.3 Asymptomatic gonorrhoea and chlamydia infections in men who have sex with men ........................................................................................................................ 7 2.3.1 Gonorrhoea Infection ............................................................................................ 7 2.3.2 Chlamydia Infection.............................................................................................. 8 2.4 Prevalence and occurrence of N. gonorrhoea and C. trachomatis ........................... 9 2.5 Rectal Cellular Changes during infection ................................................................ 9 2.6 Diagnosis of N. gonorrhoea and C. trachomatis .................................................... 10 2.6.1 Neisseria gonorrhoea.......................................................................................... 10 vi 2.6.2 Chlamydia trachomatis ....................................................................................... 11 2.7 Treatment of gonorrhoea and chlamydia ............................................................... 12 2.7.1 History................................................................................................................. 12 2.7.2 Presumptive treatment of gonorrhoea and chlamydia infections ........................ 14 2.8 Antibiotic resistance profiles of N. gonorrhoea .................................................... 14 3.0 MATERIALS AND METHODS ........................................................................16 3.1 Study Site ............................................................................................................... 16 3.2 Study Design .......................................................................................................... 16 3.3 Ethical Consideration ............................................................................................. 16 3.4 Sampling Technique .............................................................................................. 17 3.5 Study Population .................................................................................................... 17 3.5.1 Inclusion criteria ................................................................................................. 18 3.5.2 Exclusion criteria ................................................................................................ 18 3.6 Enrolment of Participants ...................................................................................... 18 3.7 Sample Size Determination.................................................................................... 18 3.8 Sample Collection .................................................................................................. 20 3.8.1 Rectal Swab ........................................................................................................ 20 3.8.2 Blood Collection ................................................................................................. 21 3.9 Laboratory Methods ............................................................................................... 21 3.9.1 Direct Smear for the detection of N. gonorrhoea ............................................... 21 3.9.2 Gene Xpert Chlamydia trachomatis / Neisseria gonorrhoea assay.................... 22 3.9.2.1 Assay Quality Control...................................................................................... 22 3.9.2.2 Assay Procedure ............................................................................................... 23 3.9.3 Culture .............................................................................................................. 23 3.9.3.1 Gram stain ........................................................................................................ 24 3.9.3.2 Oxidase test ...................................................................................................... 25 3.9.3.3 Catalase Test .................................................................................................... 25 3.9.3.4 Analytical Profile Index for Neisseria and Haemophilus ................................ 26 3.9.3.5 Antibiotic susceptibility Test ........................................................................... 26 3.9.4 HIV Test.............................................................................................................. 27 3.10 Data Analysis ....................................................................................................... 28 vii 4.0 RESULTS .............................................................................................................30 4.1 Demographic Characteristics of the Study Population .......................................... 30 4.1.1 Sexual Transmitted Infection risk characteristics of participants ....................... 32 4.1.2 Risk for sexual exposure ....................................................................................