Education and Research


Our Section meets the institution’s educational objectives by: 

  • Holding weekly ID seminars for internal medicine residents and ID fellows throughout the year. 

  • Providing daily bedside teachings to our internal medicine residents during ID rounds. 

  • Teaching internal medicine residents in the ID outpatient clinic. 

  • Supervising internal medicine resident dissertations in ID, interdepartmental research studies, and international collaborative research projects. 

  • Giving general updates in ID relevant to other providers including nurses in continuing medical and nursing education initiatives. 

  • Presenting at international and local ID conferences including those hosted by the HIV Clinicians Society of Kenya and the Infectious Diseases Society of Kenya.

Infectious Diseases Fellowship 

The Infectious Diseases (ID) Fellowship is a sub-specialty training program for doctors who have completed residency training in Internal Medicine. It is modeled after North American fellowships using Infectious Diseases Society of America (IDSA) guidelines that have been adapted to East Africa. Fellows will spend the majority of their time rotating at the Aga Khan University Hospital in Nairobi, Kenya, which has 3 full-time and 1 part-time faculty certified in ID and one of the best diagnostic and microbiological laboratories in the country.

In addition to the Nairobi-based experience, ID fellows will spend 4 months of training at the University of British Columbia (UBC) in Canada. The fellowship is 2 years in duration and includes extensive inpatient and outpatient supervised clinical experience. Graduating fellows will have expertise at the subspecialty level in a broad range of infectious diseases including HIV and AIDS, antimicrobial usage and stewardship, hospital infection control, tuberculosis (TB), and complicated inpatient and outpatient infections. 

Research is an important part of the fellowship and the fellow will engage in a research project which will be submitted for publication prior to completion of the program. Current grant-funded research projects include those in HIV drug resistance and cervical cancer screening and treatment among HIV-infected women. Other potential research topics include the study of non-communicable diseases and opportunistic infections among HIV patients as well as into the development of antimicrobial resistance and hospital-acquired infections. The ID fellowship at AKU is a unique opportunity to initiate an academic medical research career and become a nationally and internationally recognized leader in ID and HIV.

Key Responsibilities

ID training activities under ID faculty supervision include:

  • Inpatient ID clinical service and consultations from Medicine, Pediatrics, Surgery, and other departments

  • Outpatient ID clinical services including HIV, hepatitis, immunizations, and TB

  • Microbiology

  • Teaching of Medicine residents, medical students, and other trainees 

  • Participation in ID seminars and conferences

  • Participation in ID-related hospital committees including infection control and antimicrobial stewardship

  • ID research to include submission of manuscript(s) for publication

  • External ID rotations at UBC and other sites in Kenya and abroad


  • Completion of an Internal Medicine Residency

  • Eligible for registration by the Kenya Medical Practitioners & Dentists Board which must be completed before starting the fellowship

Personal Attributes

  • Good communication skills

  • Good team player

  • Learner who demonstrates good study habits and research skills

  • Demonstrates honesty, integrity, compassion and respect for diversity and ethics

  • Seeks and accepts advice and adheres to deadlines

To Apply

Applications together with a detailed Curriculum Vitae, names of three referees, telephone number, e-mail address, and copies of certificates and testimonials should be sent by email to or post to:

The Director 
Postgraduate Medical Education 
Faculty of Health Sciences 
Aga Khan University 
ETB 7th Floor 
P.O. Box 30270-00100 
Nairobi, Kenya


Current Research Projects 

  • Impact of Cryotherapy versus Loop Electrosurgical Excision Procedure (LEEP) on Recurrence of Cervical Intraepithelial Neoplasia and HIV-1 Cervical Shedding among HIV-positive Women. (2010-2018). Michael Chung.

  • Drug Resistance Testing in Kenya to Improve ART Suppression of HIV Replication: An Inexpensive Simple Assay to Detect HIV Drug Resistance. (2013-2018). Michael Chung.

  • Mechanisms & risk factors of chronic lung disease in HIV+ adolescents in Nairobi. (2017-2022). Michael Chung.

MMed Theses

  • Prevalence of HLA-B*5701 in a Kenyan Population with HIV Infection (2016). Hilda Nabiswa and Reena Shah.

  • The Diagnostic Accuracy of Determine™ TB LAM Antigen in Detection of Extra Pulmonary Tuberculosis (EPTB). (2015). Fatima Juma and Reena Shah.

  • High Prevalence of Liver Fibrosis in Patients with Human Immunodeficiency Virus Monoinfection and Human Immunodeficiency Virus Hepatitis-B Co-infection as Assessed by Shear Wave Elastography: Study at a Teaching Hospital in Kenya. (2015). Samuel Nguku and Reena Shah.

  • Pulmonary function tests in HIV patients at AKUHN. (2015). Noah Murby and Reena Shah 

  • Liver elastography in HIV/HBV co-infected patients. (2014). Samuel Nguku and Reena Shah. 

  • Cardiometabolic diseases in HIV. (2014). Eric Njenga and Reena Shah.

  • Prevalence of Transmitted Drug Resistance Mutations in HIV-1. (2012). Simon Onsongo and Reena Shah


  1. Shah R, Nabiswa H, Okinda N, Revathi G, Hawken M, Nelson M. Prevalence of HLA-B*5701 in a Kenyan Population with HIV Infection. YJINF3981. Journal of Infection Corresponding. 4-OCT-2017 DOI information: 10.1016/j.jinf.2017.09.007.

  2. Juma FO G, Waweru P, Revathi G, Nelson M, Shah R. The Diagnostic Accuracy of Determine™ TB LAM Antigen in Detection of Extra Pulmonary Tuberculosis (EPTB). J Infect. 2017 Dec;75(6):583-586. doi: 10.1016/j.jinf.2017.08.011. Epub 2017 Sep 4.

  3. Greene SA, McGrath CJ, Lehman DA, Marson KG, Trinh R, Yatich N, Nyongesa-Malava E, Kiptinness C, Richardson BA, John-Stewart GC, De Vuyst D, Sakr SR, Mugo NR, Chung MH. Increased Cervical HIV RNA Shedding Among HIV-Infected Women Randomized to Loop Electrosurgical Excision Procedure (LEEP) compared to Cryotherapy for Cervical  Neoplasia 2/3. 2017. Clinical Infectious Diseases. [original work]. In Press

  4. Silverman RA, Beck IA, Kiptinness C, Levine M, McGrath CJ, Bii S, Richardson BA, John-Stewart GC, Chohan B, Sakr SR, Kiarie JN, Frenkel LM, Chung MH. Prevalence of Pre-antiretroviral Treatment Drug Resistance by Gender, Age, and Other Factors in HIV-infected Individuals Initiating Therapy in Kenya, 2013-2014. 2017. Journal of Infectious Diseases. [original work]. In Press