Welcome to the Centre for Microbiology Research (CMR). CMR is one of the oldest research centres of the Kenya medical Research Institute (KEMRI). CMR has many laboratories spread in four sub-centres located in Nairobi (Mbagathi and Kenyatta National Hospital complex), Kisumu and the coastal town of Kwale. The centre has a total of 37 scientific and 13 support staff. In addition, the centre hosts the Nairobi centre for the Nagasaki University Institute of Tropical Medicine (NUITM) with a staff of 10. Our staff is well trained and continuous education is highly emphasized. Currently, 5 members of our team are pursuing PhD studies locally and abroad, 4 are training at Masters Level, while 3 are pursuing their BSc Higher National Diplomas. A further 2 are registered for Diplomas courses in various technical institutes.

Currently, a total of 11 research projects are underway and 3 have recently been completed. In the last two years, a total of 14 manuscripts have been published by members of our team in peer-review journals and 20 abstracts have been presented in various scientific meetings world-wide.

Our centre collaborates with many research institutes locally and internationally and this helps to expand our research capabilities. CMR houses the regional laboratory of Antimicrobial Resistance testing and Surveillance (the enteric pathogens research unit) and hosts the local chapter of Association for Prudent use of Antimicrobials (APUA). We also have a Mycology lab that carries research on fungal and opportunistic infections. Our research unit at the KEMRI headquarters is involved in travel medicine through research of travelers’ diarrhea. We are also mandated to conduct research on helminthic infections and we have conducted studies on lymphatic filariasis in coastal region of Kenya. CMR is also a member of the Global Alliance to Eliminate Lymphatic Filariasis.

The NUITM project is supported by Education, culture, sports, science and technology, Japan and has conducted a field survey on malaria and mosquitoes in Suba district. Our unit also hosts the Microbiology unit of the Institute of Tropical Infectious Disease (INTROMID). Through INTROMID, a training initiative known as Infectious Disease Research Training Program (IDRTP) was launched. This program is a joined initiative between the University of San Francisco (UCSF) and Washington, USA and the CMR’s The Research Care and Training Program (RCTP) headed by Dr. E.A. Bukusi.

CMR also carries out medical examination of employees in the hospitality industry (HISP) from hotels, schools, Manufacturing industries at the centre headquarter and in Kwale.

With this brief introduction, welcome to our website. This website is still under construction and will be upgraded regularly to reflect the goals and aspirations of KEMRI in the search of Good Health for Kenyans.


The Centre is responsible for conducting research aimed at providing solutions for the reduction of infectious, parasitic, bacterial and non-infectious diseases causing ill health in Kenyan population. To conduct microbiological research, service provision and capacity building aimed at providing solutions for the reduction of infectious disease burden:


  1. Diarrhoea: cholera, shigella, pathogenic E. Coli, salmonella-epidemiology, characterization and drug testing;
  2. Sexually Transmitted infections; aetiology, prevalence, epidemiology, control strategies;
  • HIV/AIDS – opportunistic infections, care and research in clinical trials.
  1. Other bacterial and mycotic infections: aetiology, prevalence, epidemiology, control strategies;
  2. Epidemiology of nosocomial infections; aetiology and control strategies;
  3. Antimicrobial drug resistance monitoring and surveillance, and genomics;
  • Protozoal and helminthic infections: aetiology, epidemiology, immunology, control strategies;
  • Provision of laboratory services including medical certification to hospitality industry in Kenya;
  1. Capacity building and mentorship through the postgraduate training program and collaborations and
  2. Diseases research and rapid response.
Collaborator/Partner Programme area for Collaboration
World Health Organization (WHO) Development of modules for a Standardized District Level Management NTD Training Course
Nagasaki University (NUITM/KEMRI Project) Operational research in parasitology (schistosomiasis, STH), malaria entomology, and school health
Centre for Neglected Tropical Diseases (CNTD), Liverpool School of Tropical Medicine, UK
  • Strengthening laboratory capacity of ESACIPAC for NTDs
  • Operational research in lymphatic filariasis
London School of Hygiene and Tropical Medicine, UK Research on soil-transmitted helminths control
Partnership for Child Development (PCD) Capacity building in school health and nutrition
Evidence Action/Deworm the World Supporting national school-based deworming programmes
Centers for Disease Control & Prevention (CDC) Research on soil-transmitted helminths in urban slum dwellings
Innovations for Poverty Action (IPA) Research on improvements of water quality, hygiene, sanitation, and nutrition on child health and development
RTI International Technical assistance in NTD programme implementation and operational research


To conduct research on emerging infectious bacterial diseases/opportunistic infections and molecular epidemiology of enteric parasites. The (3) three unit are namely:

  1. i) Bacterial diarrhea/AMR
  2. ii) Molecular diagnostic

iii) Outbreak rapid response

  1. b) Functions
  2. To conduct research on diarrhea illness caused by bacterial pathogens such as Cholera, Shigella, Salmonella, Pathogenic E. coli
  3. To carry out epidemiology, characterization of bacterial pathogens.
  • To carry out drug sensitivity testing of bacterial and parasitic pathogens and other microbiological agents (excluding viruses).
  1. c) Staff Establishment


The division is  headed by a Principal Research Scientist


To conduct research on Mycosis and Mycotoxin surveillance. There are

  1. i) Aflatoxins
  2. ii) Salmonella

iii) AMR surveillance



  1. To conduct research on isolation of fungal infection in humans.
  2. To conduct investigative research on aflatoxins research.
  • To carry out drug sensitivity testing of bacterial and parasitic pathogens and other microbiological agents (excluding viruses).
  1. To carry out bacterial investigations in epidemic and endemic out-breaks (epidemiology and characterization).

Opportunistic Infections and Genomics Division

To conduct research in antimicrobial resistance surveillance genomics, genetic basis of bacterial and parasitic infections epidemiology


  1. i) Epidemiology-HIV
  2. ii) NUITIM Collaboration

iii) Food handlers program



  1. To conduct molecular characterization of virulence factors of disease causing bacteria.
  2. To conduct research in resistance genes in bacterial pathogens.

iii. To conduct research in relatedness using genomics or sequences applications of bacterial organism and drug sensitivity testing


Willie Kipkemboi Sang’ PhD – Deputy Director CMR

Willie Sang’ is Bacteriologist by training, with over 30 years’ experience in designing and execution of research projects in biomedical/ human health. He is passionate about combating the Antimicrobial Resistance (AMR) menace; and has done several projects on the surveillance of AMR across Kenya to provide relevant data for policy makers.
Currently he is the Director Centre for Microbiology Research (CMR), KEMRI; Principal Investigator on several projects at CMR and Coordinator of World Bank funded project on surveillance of commonly circulating enteric pathogens in East African region (Kenya, Uganda, Tanzania, Burundi and Rwanda). Sang’ is an Appointee to the East African Public Health Laboratory Networking Project (EAPHLN) Regional Advisory Panel (RAP), a member of the EAC Regional Networks of Mobile
Public Health Reference Laboratories for Communicable Diseases and Anti-Microbial Resistance Surveillance and Response Project- 2019-2025 and a Lecturer in Medical Microbiology at JKUAT-
ITROMID (KEMRI Station). Sang’ is a member of the National Biological Resource Committee (KEMRI representative) and KEMRI Committee member for advocating for rights of minority groups (people with disabilities)


1. Justine Nyasinga, Cecilia Kyany’a, Raphael Okoth, Valerie Oundo, Daniel Matano, Simon Wacira, Willie Sang, Susan Musembi and Lillian Musila. A six-member SNP assay on the iPlex MassARRAY platform provides a rapid and affordable alternative for typing major African Staphylococcus aureus types. Access Microbiology .May 2019
2. Kivata M, Mbuchi M, Eyase F, Bulimo W, Kyanya CK, Oundo V, Muriithi SW, Andagalu B, Mbinda W, Soge O, McClelland R, Sang W, Mancuso. gyrA and parC mutations in fluoroquinolone-resistant Neisseria gonorrhoeae isolates from Kenya. BMC Microbiol. 19(1):76. April 2019

3. Too J.R., Ngari M., Kikuvi G.M., Matey E.J., Koima J., Chebii J.,Wanzala P., Kiptoo M.K., Githui W.A. and Sang W.K (2017): Prevalence, virulence genes and Antimicrobial Resistance of Shiga-toxigenic E.coli in diarrhea patients from Kitale, Kenya. Afr J Health Sc, 30 (2): 105-119.
4. Matey EJ, Tokoro M, Mizuno T, Matsumura T, Nagamoto T, Bi X, Oyombra JA, Sang WK, Songok EM, Ichimura H. AIDS. Positive correlation of HIV infection with Giardia intestinalis assemblage B but not with assemblage A in asymptomatic Kenyan children. AIDS 2016, 30:2385–2387.
5. Matey EJ, Tokoro M, Nagamoto T, Mizuno T, Saina MC, Bi X, Oyombra JA, Okumu P, Langat BK, Sang WK, Songok EM, Ichimura H. AIDS. Lower prevalence of Entamoeba species in children with vertically transmitted HIV infection in Western Kenya. AIDS 2016, 30:803–805.

Dr. Onono Picture

Dr.Maricianah Onono

Dr.Maricianah Onono is a medical doctor and research scientist with over 15 years’ experience in clinical practice and research in the field of Sexual, Reproductive, Adolescent and Child Health (SRACH). She has worked with Kenya’s Ministry of Health (MoH) and the Kenya Medical Research Institute (KEMRI).

She coordinates the implementation, research, monitoring and evaluation activities of several programs and clinical trials to provide evidence that can be translated into policy in Kenya. In addition, she has served as a consultant for the World Health Organization (WHO) and the United Nations Children’s Fund (UNICEF).


1. Onono M, Odhiambo G, Congo O, Waguma LW, Serem T, Owenga MA, and Wekesa P. Narratives of women using a 24-hour ride-hailing transport system to increase access and utilization of maternal and newborn health services in rural western Kenya: a qualitative study. American Journal of Tropical Medicine and Hygiene. 2019 Sep 23. doi: 10.4269/ajtmh.19-0132. [Epub ahead of print]

2. Iris Wanga, Lisa Abuogi, Eluid Akama, Elizabeth A. Bukusi, Anna Helova, Pamela Musoke,Wafula Nalwa, Thomas Odeny, Janet M. Turan, and Maricianah Onono. Acceptability of community-based mentor mothers among HIV-positive pregnant women and partners in the context of Option B plus in Kenya. BMC Pregnancy Childbirth. 2019 Aug 13;19(1):288. doi: 10.1186/s12884-019-2419-z. PMID 31409297

3. Onono M, Wekesa P, Adhu CK, Waguma LW, SeremT, Owenga MA, and Ong’wen P, 2019. Effects of an expanded Uber-like transport system on access to and use of maternal and newborn health services: findings of a prospective cohort study in Homabay, Kenya BMJ Glob Health. 2019 May 13;4(3):e001254. doi: 10.1136/bmjgh-2018-001254. eCollection 2019. PMID:31179030


Prof. Bukusi, Elizabeth Anne
Research Scientist

Prof. Bukusi’s primary research focuses is on Sexually Transmitted Infections; Reproductive Health; and HIV Prevention, Care, and Treatment. In 1995, Prof. Bukusi and other partners established the Research Care and Treatment Program at KEMRI. In addition to conducting research, the program aims to enhance local capacity to conduct socio-behavioral and biomedical research and provide HIV care through training and infrastructure development. In addition to her substantial experience conducting research in Kenya, providing HIV care, and mentoring and training different cadres of health care and research personnel, Prof. Bukusi has an interest in ethics and the development of systems and structures for regulating research in the institute and the country. She chaired the Scientific Steering Committee at KEMRI and oversaw scientific regulation at KEMRI between 2011 and 2016. She also steered the restructuring of the research regulation system at KEMRI, revising the research guidelines, improving investigator education, and instituting a mechanism for monitoring approved research projects. She served on the Data and Safety Monitoring Boards for the MIRA (diaphragm) study and the CAPRISA 004 trial, previously chaired the Kenya HIV and AIDS Research Coordinating Mechanism of the National AIDS Control Council, and currently serve on the Kenya National HIV Prevention Task Force. Prof. Bukusi served on the World Health Organization’s Department of Reproductive Health Scientific Technical Advisory Group from 2008 to 2014, and currently serve as the HRP Alliance chair person. She was the inaugural chair of KEMRI’s Sexual, Reproductive, and Child Health Program Committee (SRACH) from inception to 2014, and co-chaired the HIV Prevention Trials Network’s Women at Risk Committee between 2012 and 2014. Prof. Bukusi currently serve as the first non-South African to be appointed to the South African Medical Research Council Board of Management for a second three year term. Over the past decade Prof. Bukusi and her team have conducted pivotal HIV prevention studies with colleagues from the University of Washington, including the Partners PrEP Study, the Partners Demonstration Project, and the ongoing Partners Scale-up Project that has been central to the development of PrEP guidance for populations worldwide.

Contribution to Science
1. Prof. Bukusi’s early work on the effect of pelvic inflammatory disease among HIV infected women contributed to recommendations of treatment of mild PID among women with HIV as outpatient oral medication. As a follow up her subsequent work on Bacterial vaginosis and the association male partners and recurrence of BV contributed to better understanding of socioeconomic factors affecting female genital hygiene.
2. The expansion of HIV care within the region in Kenya with the highest HIV prevalence and the platform for research in various aspects of HIV care/integration and socioeconomic concerns have led to improving health outcomes for those living with HV in the region and contributing to scientific output.
3. Her work in the fishing community where the HIV prevalence is highest in Kenya has contributed to understanding of risk factors in this key population and formulating possible interventions to mitigate the high rate of infection transmission.
4. She was part of the Partners PrEP Study that demonstrated the use of PrEP for prevention of HIV among discordant couples. The Kisumu site for which Prof. Bukusi was the PI was audited by the US FDA.

Prof. Samuel Kariuki

Prof. Sam Kariuki (PhD Tropical Medicine)

Prof. Sam Kariuki is a Director in charge of Research and Development and a scientist at the Centre for Microbiology Research at KEMRI in Nairobi and a Wellcome Trust Sanger Institute International Fellow. He is a visiting Professor of Tropical Microbiology, Nuffield Department of Medicine, and University of Oxford, UK. He is the co-coordinator of Medical Microbiology Postgraduate course at the Institute of Tropical Medicine and Infectious Diseases, KEMRI.
Prof. Kariuki has research interest in the epidemiology and antimicrobial resistance of enteric bacterial pathogens, including invasive Non-Typhoidal Salmonellosis (NTS) and typhoid fever, Shigella spp, Vibrio cholerae and Escherichia coli. He is Chair, Global Antimicrobial Resistance Partnership (GARP)-Kenya chapter and in 2014-16, led the initiative for development of the Situational Analysis on AMR in Kenya culminating in the National Action Plan Draft document. He has authored/co-authored over 130 papers in peer- reviewed journals and three text books on Antimicrobial Resistance and Food Safety.

Selected Publications

1. Kariuki S, Dougan G. Antibacterial resistance in sub-Saharan Africa: an underestimated emergency. Ann N Y Acad Sci. 2014; 1323(1):43-55.
2. Kariuki S, Revathi G, Kiiru J, et al. Typhoid in Kenya is associated with a dominant Multidrug-Resistant Salmonella enterica Serovar Typhi haplotype that is also widespread
in Southeast Asia. J Clin Microbiol. 2010; 48(6):2171-6.
3. Kariuki S, Revathi G, Kariuki N, Kiiru J, Mwituria J, Muyodi J, Githinji JW, Kagendo D, Munyalo A, Hart CA. Invasive multidrug-resistant non-typhoidal Salmonella infections in
Africa: zoonotic or anthroponotic transmission? J Med Microbiol. 2006; 55:585-91.
4. Kariuki S, Revathi G, Kiiru J, Lowe B, Berkley JA, Hart CA. Decreasing prevalence of antimicrobial resistance in non-typhoidal Salmonella isolated from children with
bacteraemia in a rural district hospital, Kenya. Int J Antimicrob Agents. 2006; 28:166-
5. Kariuki, S., G. Revathi, N. Kariuki, J. Kiiru, J. Mwituria, Charles A Hart. Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal
infections in children admitted to hospital in Nairobi, Kenya. BMC Microbiology 2006, 6:101 (15 Dec 2006). PMC1764016


Dr. Robert S. Onsare

Academic Profile Summary

He holds a Ph.D. in Medical Microbiology from Jomo Kenyatta University of Technology (JKUAT) (2015) Novartis Vaccines Institute for Global Health, Italy (Currently GSK Vaccines Institute for Global Health); Title of Thesis: “Genomic and immunological characterization of clinical isolates of Nontyphoidal Salmonella (NTS) from Kenya”. His Master of Science also in Medical Microbiology, is also from JKUAT in 2010 (Title of Thesis: Plasmid and Integron Analysis of Multi-drug Resistant Strains of Non-typhoid Salmonella Isolated from Patients in Nairobi, Kenya).

Dr. Onsare received his Bachelor of Science (Hons) from Egerton University in 2006 in Biochemistry, Chemistry & Zoology.

Current Research Interests:
Whole-genome based characterization (Genomics), Antimicrobial Resistance, Immunology and Epidemiology of Nontyphoidal Salmonella (NTS) and Typhoid fever and other key tropical enteric bacteria including Shigella spp, Vibrio cholerae and Escherichia coli.
Selected Publications
1. ONSARE, R. S. & MACLENNAN, C. A. 2014. New
genomics studies to understand the link between
nontyphoidal Salmonella bacteremia and gastroenteritis in Africa. J Infect Dev Ctries, 8, 252-3.
Relationship between Antibody Susceptibility and Lipopolysaccharide O-Antigen Characteristics of Invasive and Gastrointestinal Nontyphoidal Salmonellae Isolates from Kenya. PLoS Negl Trop Dis, 9.
3. Kariuki, S & Onsare, R. S. (2015). Epidemiology and Genomics of Invasive Nontyphoidal Salmonella Infections in Kenya. Clinical Infectious Diseases, vol. 61 Suppl 4, pp. S317-24.

IRUNGU, P. & MITEMA, E. 2013. Improving food
safety in meat value chains in Kenya. General interest paper: FAO/WHO project report.


Profile – Dr. Mwaniki is a Medical Microbiologist at the Center for
Microbiology Research (CMR) with a PhD training in Microbiology, a Masters in Science degree in Biotechnology and a Bsc. in Biomedical Sciences and Technology.
His area of research is microbiology, development of rapid Point of Care Diagnostic Tools (POCT), and Molecular Epidemiology of (Re)-Emerging Infectious Diseases (EID) focusing on Neglected Zoonotic Diseases (NZDs), mainly the bioterrorism potential diseases (Q fever, Brucellosis, Tularemia and Anthrax).
As the Principal Investigator (PI), Dr. Mwaniki is collaborating with scientists and epidemiologists from KEMRI, Friedrich-Loeffler-Institut (FLI), Friedrich-Schiller-Universität(FSU), and International Livestock Research Institute (ILRI) through a joint DAAD- IFPRI (through ILRI)-FLI-FSU funded research grant.

“Our study is investigating the Etiologies of acute febrile illness in patients seeking health care in pastoral dominant regions of Kenya targeting Q fever, Brucellosis, and Tularemia in which we hope to advance our understanding on the epidemiology of above zoonotic pathogens, their relative contributions in causing acute febrile illnesses (fevers of unkown origin) and the risk factors involved in the pathogen transmission, persistence and spread in human populations.
– The overall goal is to provide best scientific-based evidence essential for appropriate policy formulationstowards cost-effective control strategies for NZDs, and
development of sensitive and specific rapid affordable diagnostic methods applicable in resource limited settings”, Dr. Mwaniki explains.

Selected Publications:

1. Njeru J, Tomaso H, Mertens K, Henning K, Wareth G,
Heller R, Kariuki S, Fèvre E, Neubauer H, Pletz M: Serological evidence of Francisella tularensis in febrile patients seeking treatment at remote hospitals, Northeastern Kenya, 2014-2015. New Microbes and New Infections. 2017, June: doi: 10.1016/j.nmni.2017.05.015
2. de Glanville WA, Conde-A´lvarez R, Moriyo´n I, Njeru J, Dı´az R, Cook EAJ, et al. Poor performance of the rapid test for human brucellosis in health facilities in Kenya. PLoS Neglected Tropical Diseases. 2017, 11(4): e0005508. pntd.0005508
3. Jamil T, Melzer F, Njeru J, El-Adawy H, Neubauer H,
Wareth G: Brucella abortus: Current Research and Future Trends. Current Clinical Microbiology Reports. 2017, 4(1):1-10. doi: 10.1007/s40588-017-0052-z
4. Njeru J, Wareth G, Melzer F, Henning K, Pletz MW, Heller R, Neubauer H: Systematic review of brucellosis in Kenya: disease frequency in humans and animals and risk factors for human infection. BMC Public Health 2016, 16(1):853.
5. Njeru J, Melzer F, Wareth G, El-Adawy H, Henning K, Pletz MW, Heller R, Kariuki S, Fevre E, Neubauer H: Human Brucellosis in Febrile Patients Seeking Treatment at Remote Hospitals, Northeastern Kenya, 2014-2015. Emerging infectious diseases 2016,
22(12):2160-64. doi: 10.3201/eid2212.160285.


Mr. Abdi Mohamed
Designation: Research Officer

Profile Academic and professional qualifications:
Mr. Mohamed has a Master of Science in Molecular Biology from Vrije Universiteit Brussel in Belgium (2006 – 2008) and a Bachelor of Science in Biomedical Science and Technology, Egerton University, Kenya (1997 – 2003).
Professional/work /Research Experience:
Research Officer, Mycology and Opportunistic Infections Laboratory, CMR, KEMRI. Aug 2010 – to date
Assistant Research Officer, Mycology and Opportunistic
Infections Laboratory, CMR, KEMRI. Aug 2003 – Jul 2009. KEMRI/JICA Infectious Diseases Research Program,

Projects worked/working on:

1. Mapping antifungal resistance project, KEMRI, Co-investigator 2017 to
date. Investigating on fungal respiratory involvement in recurrent/chronic Non TB respiratory infections in Kenya, towards targeted therapy.
2. EpiCrypto Project, KEMRI , Principal Investigator, 2015- 2017
Molecular Epidemiology of Cryptoccocal Meningitis in Kenya. Investigating on Cryptococcal strain variants towards future diagnostic applications in addition to antifungal resistance and virulence characteristics.
3. SToP Crypto Project, KEMRI, Co-investigator, 2012-2015.
A Randomized Clinical Trial Comparing Flucytosine-Fluconazole Combination Therapy to Fluconazole Alone for Asymptomatic Cryptococcal Antigenemia in Western Kenya. Investigating on the efficacy and safety of antifungal treatments for asymptomatic cryptoccocal infections in advanced HIV Population.
4. KEMRI/JICA Infectious Disease Research Project, Laboratory Research Assistant, 2004-2006

Selected Publications /papers presented
Abdi M, Cornelis P and Tiffany V. The Pseudomonas aeruginosa OxyR regulator: A potential therapeutic target. 3rd EAHSC 2009.
A. Mohamed, L.Muita, T.Ouko, C.Bii, B.Obanda, E. Amukoye, N.Wamae, M.Njoroge, O.Mashedi, T.Ukon,Y.Kanamoto. Opportunistic diseases in adults on HAART and Cotrimoxazole prophylaxis in Nairobi, Kenya. 26th AFHESC, 2005.
Mohamed A, Osidiana V, Amukoye E, Wamae N, Adungo I and Kanamoto
Y. Prevalence of Chlamydia trachomatis antibodies in rural Western Kenya. 26th AFHESC 2005.

Research Grants/Current/Previous last three (3) years. KEMRI IRG No. 115/4 – Principal Investigator
KEMRI IRG No. – Co-investigator
NIH, Forgaty grant No; K01TW008764 – Co-investigator.



Academic summary:

PhD (Bio-Science Engineering, KuLeuven, Belgium), MSc (Molecular Biology, KuLeuven, Belgium), MSc (Microbiology, UoN – Nairobi), BSc (Bio. Sci UoN – Nairobi)

Dr. John Kiiru has over 10 years of experience as a researcher at the Kenya Medical Research Institute (KEMRI) at the Centre for Microbiology Research. His research objective is to mapping the spread of infectious diseases with a special focus on Multi-Drug Resistant (MDR) strains using integrated Epidemiology and Molecular Biology strategies. He is the Scientific leader of the newly formed Consortium for Pathogen Epidemiology, Ecology and Genomes (CoPEEG). His current interests include environmental component of Antimicrobial resistance and development of algorithms that can be use to predict, manage and prevent outbreaks of zoonotic nature that include Anthrax, Cholera, Brucellosis and campylobacter. He has published on Salmonella, E. coli, and Vibrio among other pathogens with special focus on mobile genetic elements and extended spectrum beta-lactamases.

He is also a faculty member of the Wellcome Trust International Training Programs in molecular aspects of infectious pathogens. He also teaches various themes in molecular microbiology at the KEMRI/JKUAT ITROMID post-graduate course and is an invited lecturer in JKUAT and University of Nairobi. He is a member of the National Infectious and Parasitic Diseases Research Program (IPDRP) and has recently completed a Post-Doctoral research with the University of Liverpool/KEMRI/UoN/ILRI Zoonotic and Emerging Diseases Program.

Selected Publications

Kariuki S, Okoro C, Kiiru J, Njoroge S, Omuse G, Langridge G, Kingsley RA, Dougan G, Revathi G. Ceftriaxone-Resistant Salmonella enterica Serotype Typhimurium Sequence Type 313 from Kenyan Patients Is Associated with the blaCTX-M-15 Gene on a Novel IncHI2 Plasmid. Antimicrob Agents Chemother. 2015 Jun;59(6):3133-9. doi: 10.1128/AAC.00078-15. Epub 2015 Mar 16.



1. Senior Research Officer, Kenya Medical Research Institute (KEMRI), Nairobi
2. Coordinator, CMR Laboratory Services Project, Centre for Microbiology Research/KNH Unit (RG)
3. Lecturer in Epidemiology (TPH-3100), ITROMID, JKUAT, Nairobi

Positions and Honors
1999 – 2001 Medical Officer, Kenyatta National Hospital, Nairobi, Kenya 2003 – 2004 Company Doctor, Strategies Health, Nairobi, Kenya
2003 – 2004 Accident and Emergency Doctor, Mater Hospital, Nairobi, Kenya
2004 – Present Senior Research Officer, Kenyan Medical Research Institute, Nairobi, Kenya

B) Publications

(1) Wamae CN, Njenga SM, Ngugi BM, Mbui J and Njaanake HK. Evaluation of effectiveness of diethylcarbamazine/albendazole combination in reduction of Wuchereria bancrofti infection using multiple infection parameters. Acta Trop. 2010 Oct 8 [PubMed PMID:0933491].
(2) Ngugi BM, Hemmerling A, Bukusi EA, Kikuvi G, Gikunju J, Shiboski S, Fredricks DN and Cohen RC. Effects of BV-Associated Bacteria and Sexual Intercourse on Vaginal Colonization with the Probiotic Lactobacillus crispatus CTV-05. Sex. Trans. Dis. 2011
(3) Mary A. Uyoga, Simon Karanja, Daniela Paganini, Colin I. Cercamondi, Sophie A. Zimmermann,
Benjamin Ngugi, Penny Holding, Diego Moretti, Michael B. Zimmermann. Duration of exclusive breastfeeding is a positive predictor of iron status in 6- to 10-month-old infants in rural Kenya. Maternal & Child Nutrition. 2016
(4) BN Lowoko, BM Ngugi, A Mala1 And JK Mutai. Factors Associated With Intestinal Parasites Among School Going Children in Lodwar Municipality, Turkana County, Kenya. East African
Medical Journal Vol. 91 No. 1 January 2017

C) Work in Progress
(1) Kiiru JN, Ngugi BM, Ouko TT and Mwaniki JN. Combining molecular, serologic and epidemiologic strategies to investigate risk factors for high priority (Re)-emerging infectious
bacterial epidemic diseases (Cholera, Campylobacteriosis, Anthrax, and Brucellosis, [CCAB] in
selected high risk regions in Kenya” (Proposal in progress to be submitted for funding).
(2) Clinical work and Coordination of the CMR Laboratory Services Project an income generation project at the Centre for Microbiology Research, KEMRI.

D) Research/Educational support

2006 – 2010 PhD Scholar, Institute of Tropical Medicine and Infectious Diseases, Kenya Medical Research Institute (KEMRI)/Jomo Kenyatta University of Agriculture and Technology (JKUAT)

2007- 2008 Certificate Scholar, Advanced Training in Clinical Research (ATCR) Certificate Program, Global Health Sciences, University of California, San Francisco (UCSF)

2007 – 2010 Scholar, KEMRI/UCSF Infectious Disease Research Training Program (IDRTP)


Mr. Erastus Mulinge Kakundi-Research Officer

Academic Profile Summary:

PhD. Student (Applied Parasitology), UoN Molecular epidemiology of cystic echinococcosis in Kenya

Master of Science (Biochemistry), University of Kwa- Zulu Natal, South Africa, 2009.
Title of Thesis: Molecular analysis of Congopain gene family.

Bachelor of Science (Hons), Kenyatta University. (Biochemistry).

Current Research Interests:
Molecular Epidemiology and Parasitology. Specifically the use of molecular biology tools to answer epidemiological questions in human and zoonotic diseases. The one health approach in understanding disease transmission from the environment and animals to humans. Some of disease of interest include cryptosporidiosis, giardiasis, amoebiasis, cystic echinococcosis, Schistosomiasis, soil transmitted helminths and human and zoonotic Taenia species.

Selected Publications:

1. Mwendwa F, Mbae CK, Kinyua J, Mulinge E, Mburugu GN, Njiru ZK. (2017). Stem loop-mediated isothermal amplification test: comparative analysis with classical LAMP and PCR in detection of Entamoeba histolytica in Kenya. BMC Res Notes. 10(1):142

2. Mbae C, Mulinge E, Guleid F, Wainaina J, Waruru A, Njiru ZK, Kariuki S. (2016). Molecular Characterization of Giardia duodenalis in Children in Kenya. BMC Infect Dis. 16, 135.

3. Mbae C, Mulinge E, Waruru A, Ngugi B, Wainaina J, Kariuki
S. (2015). Genetic Diversity of Cryptosporidium in Children in an Urban Informal Settlement of Nairobi, Kenya. PLoS One. 10, (12).

4. Odero, J., Magambo, J., Zeyhle, E., Kutima, H., Ndahi, L., Njonge, F., Mutwiri, T., Mbaya, H., Mbae, C., Mulinge, E., Kagendo, D., Kern, P., Romig, T., (2014). The monetary burden of cystic echinococcosis and its distribution based on gender and age in Turkana North District, Kenya. Asian. J. Pharm. Hea. Sci. 4(4), 1135 – 1142.

5. Mbaya, H., Magambo, J., Njenga, S., Zeyhle, E., Mbae, C., Mulinge, E., Wassermann, M., Kern P., Romig, T., (2014). Echinococcus spp. in central Kenya: a different story. Parasitol. Res. 113(10), 3789-3794.



Academic Profile Summary:

Ph.D. (Medical Molecular Parasitology), Open University, UK, 2014. Title of Thesis: “Genetic diversity of Cryptosporidium and Giardia in children with and without HIV in informal settlements of Nairobi, Kenya” Master of Science (Medical Parasitology), JKUAT, 2004;
Bachelor of Science (Hons), JKUAT, 1997 (Biochemistry
& Zoology).
Current Research Interests:
-Emerging/Neglected infectious parasitic diseases and
opportunistic infections, detection, Identification and surveillance.
Molecular epidemiology of enteric parasites e.g. Cryptosporidium, Giardia, Cyclospora, Isospora, Microsporidia, Echinoccocus, Schistosomiasis and other geohelminthes.
Work on emerging infectious diseases in animal health. Hydatidology
Mentorship programmes


1) Fridah Mwendwa , Cecilia K. Mbae , Johnson Kinyua , Erastus Mulinge , Gitonga Nkanata Mburugu4 and Zablon K. Njiru. Stem loop- mediated isothermal amplification test: comparative analysis with classical LAMP

and PCR in detection of Entamoeba histolytica in Kenya. BMC Research Notes,(2017) 10:142 DOI 10.1186/s13104-017-2466-3
2) Zablon K. Njiru, Cecilia K. Mbae, and Gitonga
N. Mburugu. Loop-Mediated Isothermal Amplification Test for Trypanosoma gambiense Group 1 with Stem Primers: A Molecular Xenomonitoring Test for Sleeping Sickness Journal of Tropical Medicine
Volume 2017 (2017), Article ID 8630708, 7 pages

3) Regina Njeru. Cecilia Mbae , Samuel Kariuki , Betty E Owor, Simon Karanja. Prevalence of Group a Rotavirus before and after Vaccine Introduction in Mukuru Informal Settlement in Kenya. Journal of Biology, Agriculture and Healthcare ISSN 2224-3208 (Paper) ISSN 2225-093X (Online) Vol.6, No.14. 2016
4) Mbae C, Mulinge E, Guleid F, Wainaina J, Waruru A, Njiru ZK, Kariuki S.
Molecular Characterization of Giardia duodenalis in Children in Kenya. BMC Infect Dis. 2016 Mar 22;16(1):135. doi: 10.1186/s12879-016-1436-z.
5) Gikonyo N.J, Nyangao O.J, Mbae C, Ngeranwa J, Njagi N.M.E, Kariuki M.S. Prevalence of group A rotavirus, enteric adenovirus, norovirus and astrovirus infections among children aged five years and below in Mukuru slums Nairobi Kenya. [Afr J Health Sci. 2016; 29(1):134-145]



Designation: Chief Laboratory Technologist (CLT)
Profile – Academic and professional qualifications
MSc, PhD © on Infectious Diseases and Vaccinology (on-going)

Professional/work /research experience
i. Molecular epidemiology of causes of infectious diseases of bacterial and mycological origin focusing on drug resistance surveillance, control and management.
ii. Bioassays on traditional medicinal plant extract towards development of new drugs.
iii. Quality Control and Quality Assurance on systems in Medical Laboratories.

iv. Sharing and dissemination of knowledge in the current dynamic scientific setting hence have participated in a number of research programs and facilitated workshops on Good Laboratory Practices in collaboration with the Ministry of Health as part of human resource capacity development mainly in the field of infectious disease management by diagnosis.

– The main project engagement currently is multi-central on Epidemiology, Ecology and Socio-Economics of Disease Emergence in Nairobi and is supervising the Microbiology arm of the study.
– Microbiological / Mycological investigations using molecular, culture and immunological systems, Mycotoxin assays and bioassays on traditional plant extract towards drug development.
– Development and review of research protocols


1. Ouko TT, Ngeranwa JN, Orinda GO, Bii CC, Amukoye E, Lucy M,

Wamae CN Oxacillin resistant Staphylococcus aureus among HIV infected and non-infected patients in Kenya. East Afr Med. J. 2010; 87


2. Talaam, KK, Kirui, MC, Nga’ng’a, ZW, Olga, M, Ouko, T and Bii, CC. Mycological quality of ‘Mursik’ Collected from Soliat Location, Kericho County, Kenya. African Journal of Health Sciences, Volume 27, Number 2, April-June 2014.
3. C.C. Bii, Ouko TT, E. Amukoye, and L.W. Githinji (2002). Antifungal

drug susceptibility of Candida albicans. East African Medical Journal. 79(3): 143-145.
4. J.M. Chakaya, C. Bii, L. Ng’anga’, E. Amukoye, Ouko TT, L. Muita, S. Gathua, J. Gitau, Odongo, J.M. Kabanga, K. Nagai, S. Suzumura and Y. Sugiura. (2003). Pneumocystis Carinii pneumonia in HIV/AIDS patients at an Urban District Hospital in Kenya. East African Medical Journal. 80(1): 30-35.
5. CC Bii, J. Kose, H. Taguchi, E. Amukoye, Ouko TT, L. Muita, O. Mugasia, NC Wamae, S. Kamiya. Pneumocystis jirovecii and microbiological findings in children with severe pneumonia in Nairobi, Kenya.

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Kenya Medical Research Institute

Centre for global health research

P.O Box 20778-00202 Kisumu Tel: +254 020 2726781

+254 020 2722541, +254 020 2713349, 0722205901



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