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Characterization of Mycobacteria Spp. and Antimycobacterial Activities of Plant Derived Compounds from Anacardiaceae Family

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Characterization of Mycobacteria Spp. and Antimycobacterial Activities of Plant Derived Compounds from Anacardiaceae Family CHARACTERIZATION OF MYCOBACTERIA SPP. AND ANTIMYCOBACTERIAL ACTIVITIES OF PLANT DERIVED COMPOUNDS FROM ANACARDIACEAE FAMILY by PRUDENCE NGALULA KAYOKA Submitted in accordance with the requirements for the degree of DOCTOR OF PHILOSOPHY in the subject ENVIRONMENTAL SCIENCE at the UNIVERSITY OF SOUTH AFRICA SUPERVISOR: Prof L J MCGAW SUPERVISORS: Prof J N ELOFF AND PROF C L OBI NOVEMBER 2016 ii DECLARATION Name: Dr P N PRUDENCE KAYOKA Student number: 44414021 Degree: PhD in Environmental Science Exact wording of the title of the thesis as appearing on the copies submitted for examination: CHARACTERIZATION OF MYCOBACTERIA SPP. AND ANTIMYCOBACTERIAL ACTIVITIES OF PLANTS DERIVED COMPOUNDS FROM ANACARDIACEAE FAMILY I declare that the above thesis is my own work and that all the sources that I have used or quoted have been indicated and acknowledged by means of complete references. Signed 8/02/2017 _______________________ _______________________ SIGNATURE DATE iii DEDICATION This research is dedicated to all tuberculosis sufferers. I also dedicate this work to my late father, Raphael Kabongo for teaching me resilience and work ethics, to my mother, Therese Kabongo for teaching me the values that are leading my life and to my son, Axel Kayoka, and daughter, Benissa Kayoka, my best friends; you have been part of my life’s goals motivation from the time you were born up to date. May this work inspire you to persevere in reaching your goals and live your dreams to the mutual benefit of communities. Happy is the man who finds wisdom and the man who gains understanding: Proverbs 3:13. iv ACKNOWLEDGEMENTS There is no stand-alone individual in the universe as we are the result of so many interactions at each stage of our lives. I will not be able to remember each factor that has contributed to this PhD. Nevertheless, I wish to express my appreciation to the following individuals and/organizations: Promoter, Prof L.J. McGaw: for your unconditional availability, your guidance, technical inputs and overall support throughout the course of this study. Co-promoter, Prof J.N. Eloff: for the advice, technical input, mentoring and guidance. Your open door policy and guidance step by step through some of the experiments were very helpful in the understanding of the assays. Co-promoter, Prof C.L. Obi: for believing in me and my research proposal from the initial stage and encouraging me to pursue my degree despite all the difficulties encountered and for your support, guidance and technical inputs. Dr Matt Ekron: for organizing sample collection from infected herds. Drs Johann Kotze, Jacoba Wessels and Melinda Hansen: for providing samples. Ms Emmerentia Mkhize and Mrs Tharien de Winnaar: for carrying out administrative work in the Phytomedicine Programme. My fellow postgraduate students: for maintaining a team spirit and an environment conducive to learning in the Phytomedicine Programme. Dr Ahmed Aroke Shahid: for assisting during the last round with the laborious separation of compounds. Prof Vinesh Maharaj, Dr Mamoalosi Selepe from University of Pretoria and Dr Chris Van der Westhuyzen from CSIR: for assisting with the identification and structural elucidation of the isolated compounds. v Mr Reckson Ramuageli and Mr William Mokgojane: for providing clean glassware and always ready to assist with relevant items when requested. Ms Annette Venter: for making sure that work in the tissue culture laboratory ran smoothly in maintaining the tissue culture collection. National Research Foundation (NRF) for financial support. Department of Agriculture, Forestry and Fisheries (DAFF): for giving the authorization for my work to be conducted. National Health Laboratory Services (NHLS): for access to their laboratory facilities and providing ATCC strains of Mycobacterium tuberculosis H37Ra, ATCC strain of Mycobacterium avium and clinical isolates of Mycobacterium tuberculosis. Prof Nontombi Mbelle, Ms Kathy Lindeque and Mrs Omowunmi Onwuegbuna: for assisting with all items needed to perform my work in the laboratory. Onderstepoort Veterinary Institute: for access to laboratory facilities and providing BCG vaccine strain of Mycobacterium bovis. Research Center for Zoonosis Control, Hokkaido University, Japan: for access to laboratory facilities. I am grateful to Professors Chie Nakajima and Suzuki who assisted with the gene sequencing and spoligotyping of the Mycobacterium isolates. Tohoku University, Graduate School of Medicine, Department of Emerging Infectious Diseases, Japan: for access to the relevant laboratory facilities and financial support. I am grateful to Prof Toshio Hattori for organizing financial support during my stay in Japan and for being a reliable mentor in all activities while in Japan. University of Pretoria: for access to laboratory facilities in the Department of Paraclinical Sciences, Phytomedicine Programme and access to my promotors. University of South Africa: for allowing me time out to complete my studies and financial support. vi Lastly, my two best friends, Axel and Benissa Kayoka, my children, my motivators for your encouragement, support and love during this journey. vii ABSTRACT The treatment of tuberculosis (TB) is currently a challenge due to multi- and extensively drug resistant strains of Mycobacterium tuberculosis. Mycobacterium bovis and M. tuberculosis cause clinically indistinguishable tuberculosis in humans. Both M. bovis and M. tuberculosis have been isolated from humans and animals. Plant species contain antimicrobial compounds that may lead to new anti-TB drugs. To conduct in vitro antimycobacterial assays, it is important to include current clinical isolates as new strains of bacteria might be circulating under the ongoing climate change environment. The overall goal and objectives of this study were to isolate and characterize mycobacteria species from South Africa, to test some selected plant species of the Anacardiaceae family for antimycobacterial activity using some of the newly isolated and reference strains of mycobacteria followed by cytotoxicity evaluation of the most active plant species, and finally the isolation and characterization of at least one compound from the most active and least toxic plant. This study led to the discovery of a new isolate of Mycobacterium Avium Complex species from black wildebeest. Other non-tuberculous mycobacteria and M. bovis isolates were identified from other animal species. Five out of 15 plant species screened showed good activity against Mycobacterium species. Five antimycobacterial compounds were isolated from Searsia undulata, the most active plant species. Two out of the five compounds were identified, and one compound appears to be novel, but both compounds have been isolated for the first time from Searsia undulata. An incidental finding was the potential anticancer property of extracts of Searsia undulata. Recommended future activities include isolation and identification of more active compounds from Searsia undulata which were visible in bioautography analysis, as well as synergy evaluation of antimycobacterial activities of the different compounds with current anti-tubercular drugs. Key words: Characterization, Antimycobacterial, NTM mycobacteria, Black wildebeest, MDR-M. bovis, MDR-M. tuberculosis, Anacardiaceae, Searsia undulata, Betulonic acid. ii The project involved the following steps: Isolation and characterization of Mycobacterium species A total of 80 samples from 44 animals were processed, and included samples from 12 black wildebeest (Connochaetus gnou) (n=26); 10 cattle (Bos taurus) (n=31), 1 impala (Aepyceros melampus) (n=1); 1 rabbit (Oryctolagus cuniculus) (n=2) and 20 warthog (Phacochoerus africanus) (n=20). These samples namely lymph nodes, liver, lung and kidney were obtained from slaughtered animals showing lesions suggestive of tuberculosis and positive reactors to tuberculin test (cattle only). The methods used were isolation in liquid medium using the BACTECTM MGITTM 960 system, solid media and Löwenstein Jensen slants, with glycerol and pyruvate. The isolates were further identified using the commercial kit GenoType CM/AS reverse line blot assay and DNA strip Mycobacterium identification species (Hain Life Science, Gmbh Nehren, Germany). The isolates were further characterized by multiplex PCR, spoligotyping, Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR), gene sequencing, phylogenetic analysis and antimicrobial susceptibility test of cattle isolates (M. bovis) against first line TB drugs using a Genotype MTBDRplus kit (Hain Life Science GmbH, Nehren, Germany). The samples from cattle yielded 15 isolates of M. bovis; 8 out of the 15 isolates (53%) were resistant to isoniazid (INH) and rifampin (MDR-M. bovis), whereas 7 out of 15 (47%) were sensitive to both drugs. The presence of MDR-M. bovis is of concern as M. bovis causes tuberculosis in humans which is clinically indistinguishable from TB caused by M. tuberculosis. Added to this, there are very few data available in South Africa reporting human tuberculosis caused by M. bovis. The isolates from cattle were genotyped and yielded two spoligotypes, namely SB0121 (67%) and SB 1235 (33%). The VNTR was type 1. These isolates were from the same origin and most likely belonged to the Kruger National Park cluster as reported by Hlokwe et al. 2014. The first batch of samples, received in February 2009, from black wildebeest yielded non-tuberculous mycobacteria: a novel Mycobacterium Avium Complex species was confirmed by gene sequencing and
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