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Molecular Characterization of Streptococcus

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MOLECULAR CHARACTERIZATION OF STREPTOCOCCUS AGALACTIAE ISOLATED FROM PREGNANT WOMEN IN THE EASTERN CAPE, SOUTH AFRICA AND WINDHOEK, NAMIBIA AND ANTIBACTERIAL ACTIVITIES OF SOME MEDICINAL PLANT EXTRACTS ON THE ISOLATES MUNYARADZI MUKESI DEPARTMENT OF BIOCHEMISTRY AND MICROBIOLOGY FACULTY OF SCIENCE AND AGRICULTURE UNIVERSITY OF FORT HARE ALICE, 5700 SOUTH AFRICA 2018 i DECLARATION I, the undersigned, declare authorship of this thesis entitled “Molecular characterization of Streptococcus agalactiae isolated from pregnant women in the Eastern Cape, South Africa and Windhoek, Namibia and antibacterial activities of some medicinal plant extracts on the isolates” submitted to the University of Fort Hare for the degree of Doctor of Philosophy in Microbiology in the Faculty of Science and Agriculture. The work contained herein is my original work, with exemptions to the citations and that the work has not been submitted to any other University for the award of any degree or examination purposes. Name: Munyaradzi Mukesi Signature: ……………………………………………………………. Date: ………………………………………….. ii DECLARATION OF PLAGIARISM I, Munyaradzi Mukesi, student number: 201415927 hereby declare that I am fully aware of the University of Fort Hare’s policy on plagiarism and I have taken every precaution to comply with the regulations. Signature: ………………………………………………… Date: …………………………… iii CERTIFICATION This thesis titled “Molecular characterization of Streptococcus agalactiae isolated from pregnant women in the Eastern Cape, South Africa and Windhoek, Namibia and antibacterial activities of some medicinal plant extracts on the isolates” meets the regulation governing the award of degree of Doctor of Philosophy of the University of Fort Hare and is approved for its contribution to scientific knowledge. ……………………………….. ………………… Prof CL Obi (Supervisor) Date ………………………………. ………………… Prof SR Moyo (Co-supervisor) Date ……………………………… ………………… Prof AI Okoh (Co-supervisor) Date ……………………………… ………………… Dr BC Iweriebor (Co-supervisor) Date iv DEDICATION This thesis is dedicated to Cathrine, Takudzwa, Thandaza and Thandeka Mukesi and all the brave pregnant women who took part in this study in both Namibia and South Africa. Joshua 1:8 v ACKNOWLEDGEMENTS First and foremost, I would like to acknowledge The Almighty God for HE is and without Him nothing could be what it is. I would like to express my profound gratitude to my supervisor, Professor CL Obi for giving me lifelong lessons during our engagements throughout this study. His patience, persistence, understanding, work ethic and most of all, insightful advice, is second to none. I will forever be indebted and grateful to Professor AI Okoh for fitting me seamlessly into a wonderful group of researchers titled Applied and Environmental Microbiology Research Group (AEMREG), and giving me unconditional access to his research laboratory and facilities and treating me as one of his very own biological children. I am also grateful to the South Africa Medical Research Council (SAMRC) for support towards the purchase of some consumables. I cannot afford to forget the care and concern that his wife showed towards me. To Dr BC Iweriebor, this thesis could not have been worth a penny without your encyclopaedic knowledge. You held my hand through this and enabled me to learn invaluable techniques which have changed and moulded me. Only the Lord in Heaven can pay the debt I owe you especially for the lessons you have ingrained in me. I extend my gratitude to Professor UU Nwodo for his immense knowledge and contribution towards my studies and always keeping his door open for me. His expertise, understanding and patience helped to make me feel at home and to focus. My heartfelt thanks go to Professor SR Moyo for being a mentor and for his support and strong belief in my abilities. I would like to thank my family for their unwavering and unconditional support and belief in my abilities and for praying for me. The road was not without its challenges but they were always there to fall back on. To all my colleagues who contributed in all forms, you are well appreciated and may the Lord continue to guide you as you continue to work to fulfil your hearts’ desires. vi My heartfelt gratitude goes to the management and staff of Mduntsane, Dimbazi and Middle Drift clinics in the Eastern Cape, South Africa and Windhoek Central Hospital maternity ward, Windhoek, Namibia. I am indebted to the 630 pregnant women in both Namibia and South Africa who accepted the invitation to take part in this study. In conclusion, I recognize that this research would not have been possible without the financial assistance of the National Research Foundation (NRF) of South Africa, Goven Mbeki Research and Development Centre (GMRDC) of the University of Fort Hare and the National Commission for Research Science and Technology (NCRST) of Namibia. I am highly grateful for the financial support. vii LIST OF ACRONYMS ACE: Angiotensin Converting Enzyme AEMREG: Applied and Environmental Microbiology Research Group ALPs: Alpha like Proteins BBB: Blood Brain Barrier CA: Chromogenic Agar CAMP: Christie Atkins Munch Petersen CDC: Centre for Disease Control CNA: Colistine Nalidixic Acid Agar CLSI: Clinical Laboratory Standards Institute CMV: CytoMegalo Virus CNS: Central Nervous System Cov: Control of virulence CPS: Capsular Polysaccharide CSF: Cerebro Spinal Fluid DAMPs: Damage Associated Molecular Patterns DMSO: Dimethyl Sulfoxide DNA: Deoxyribo Nucleic Acid viii dsDNA: double stranded DNA ELISA: Enzyme Linked Immunosorbent Assay EOD: Early Onset Disease ESBL: Extended Spectrum Beta Lactamase FACS: Fluorescent Activated Cell Sorting FDA: Food and Drug Administration GAS: Group A Streptococcus GBS: Group B Streptococcus GBSDA: Group B Streptococcus Differential Agar GC-MS: Gas Chromatography- Mass Spectrometry GIT: Gastro Intestinal Tract GMRDC: Govan Mbeki Research Development Centre HIV: Human Immunodeficiency Virus HSV: Herpes Simplex Virus IAP: Intrapartum Antibiotic Prophylaxis ICR: Inducible Clindamycin Resistance ICU: Intensive Care Unit IKS: Indigenous Knowledge System ix IV: Intravenous LMIC: Low to Medium Income Country LOD: Late Onset Disease LTAs: Lipo Teichoic Acids LVS: Low Vaginal Swab MALDI-TOF: Matrix Assisted Laser Desorption Ionization- Time of Flight MHC: Major Histocompatibility Complex MIC: Minimum Inhibitory Concentration MLST: Multi Locus Sequence Typing MRSA: Methicillin Resistant Staphylococcus aureus NCBI: National Centre for Biotechnology Information NNA: Neomycin Nalidixic Agar NUST: Namibia University of Science and Technology OTC: Over the Counter PAMPS: Pathogen Associated Molecular Patterns PCR: Polymerase Chain Reaction PMNs: Poly Morphonuclear Neutrophils PROM: Premature Rapture of Membranes x PRR: Pattern Recognition Receptors PSA: Pseudomonas aeruginosa RNA: Ribo Nucleic Acid RS: Rectal Swab SAMRC South Africa Medical Research Council SCP: Streptococcal C5A Peptidase SDGs: Sustainable Development Goals SDS-PAGE: Sodium Dodecyl Sulfate-Poly Acrylamide Gel Electrophoresis STI: Sexually Transmitted Infection TBE: Tris/Borate/EDTA THP: Traditional Health Practitioners UFH: University of Fort Hare UK: United Kingdom UNSDGs: United Nations Sustainable Development Goals USA: United States of America WHO: World Health Organisation WTAs: Wall Teichoic Acids xi Manuscripts Submitted for Publication 1) Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2017). Antimicrobial Susceptibility of Streptococcus agalactiae isolated from pregnant women in South Africa and Namibia. BMC Complementary and Alternative Medicine. 2) Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2017). Prevalence and capsular type distribution of Streptococcus agalactiae isolated from pregnant women in Namibia and South Africa. BMC Annals of Clinical Microbiology and Antimicrobials. 3) Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2018). Molecular basis of virulence among Streptococcus agalactiae isolates from South Africa and Namibia. Iranian Journal of Microbiology. 4) Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2018). Multi locus sequence typing of Streptococcus agalactiae isolated from pregnant women in Namibia and South Africa. International Journal of Microbiology. Presentations at Conferences Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2015). Prevalence of GBS among pregnant women between 35 and 37 weeks gestation in the Eastern Cape, South Africa and Windhoek, Namibia. Namibia University of Science and Technology (NUST), Faculty of Health and Applied Sciences (FHAS) Research Day, 2015, Namibia. xii Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2016). Capsular type distribution among Streptococcus agalactiae isolates from pregnant women in Namibia and South Africa, Namibia University of Science and Technology, Faculty of Health and Applied Sciences Research Day, 2016, Namibia. Mukesi Munyaradzi, Benson C Iweriebor, Larry C Obi, Uchechukwu U Nwodo, Sylvester R Moyo, Anthony I Okoh (2016). Prevalence and capsular type distribution of Streptococcus agalactiae among pregnant women in South Africa and Namibia, National Council of Research Science and Technology (NCRST) Research Symposium 2016, Namibia. Mukesi Munyaradzi, Benson C Iweriebor,
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  • A Secondary Metabolite Drives Intraspecies Antagonism in a Gut Symbiont That Is Inhibited by Peptidoglycan Acetylation

    A Secondary Metabolite Drives Intraspecies Antagonism in a Gut Symbiont That Is Inhibited by Peptidoglycan Acetylation

    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.11.448121; this version posted June 12, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited 2 by peptidoglycan acetylation 3 1,2 1 1,3 4 1 1 4 Mustafa Özçam , Jee-Hwan Oh , Restituto Tocmo , Deepa Acharya , Shenwei Zhang , Silvette Ruiz-Ramírez , 5 Fuyong Li5, Christopher C. Cheng6, Eugenio Vivas7, Federico E. Rey7, Jan Claesen8, Tim Bugni4, Jens Walter5,6,9,10, 6 Jan-Peter van Pijkeren1,11* 7 8 1 Department of Food Science, University of Wisconsin-Madison, Madison, WI, 53706, USA 9 2 Division of Gastroenterology, Department of Medicine, University of California San Francisco, CA, 94141, USA. 10 3 Present Address: Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, 60612, USA 11 4 Department of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53706, USA 12 5 Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada 13 6 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada; 14 7 Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA 15 8 Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner 16 Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA 17 9 Department of Medicine and APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland; 18 10 School of Microbiology, University College Cork, Cork T12 YT20, Ireland.