The Effect of the Penile Microbiome on BV, GUD, and Genial Epithelial Trauma
The Afya Jozi, Afya Jamii (AJAJ) Study

PI: Supriya Mehta (UIC)
Investigators: Fredrick O. Otieno (NRHS), Robert C. Bailey (UIC), Stefan Green (UIC), Walter G. Jaoko (UoN), Greg Spear (Rush University)
Duration: August 2013 – July 2016
Status: Enrolling
Study Sites:

UNIM Research and Training Centre


National Institutes of Health; NIAID, DMID


The overall goal is to identify under what conditions the penile microbiome leads to: (1) BV in female sex partners, and (2) GUD and genital epithelial disruption in men and in their female sex partners. Within a prospective cohort of 204 heterosexual couples, the penile and vaginal microbiome will be measured four times over a one year period using high throughput pyrotag sequencing of the 16S rRNA gene.


BV, GUD, and genital epithelial trauma are common, and are strong, independent risks for HIV acquisition and transmission. MMC is not 100% effective, 67% of men worldwide are uncircumcised, and not all men will become circumcised. Antiretroviral regimens that can achieve >90% risk reduction will be difficult to implement on a population level in sub-Saharan Africa, which accounts for ~70% of new HIV infections worldwide. Because of this, we need to continue to develop simple and cost-effective interventions which can be scaled up to a population level. Defining how the penile microbiome increases risk of BV, GUD, and genital epithelial disruption has major implications for preventing these conditions, whereby pathogenic penile bacteria could be viewed as a treatable condition. Identifying specific bacteria that lead to these conditions and whether they are caused by different bacteria – is necessary for determining the appropriate classes of antimicrobials to disrupt acquisition and transmission. Interventions to improve penile microbiome health may include systemic or topical antimicrobials, microbicides incorporating cytokine modulators, or behavioural or hygiene practices that reduce bacteria associated with BV, GUD, and genital epithelial disruption. Such interventions would (1) reduce HIV acquisition and transmission through reduction of BV, GUD, and genital epithelial trauma as co-factors for infection, and (2) improve pregnancy outcomes and genitourinary health.


This study is a prospective cohort to be conducted in Kisumu, Kenya, at the UNIM Clinic. The study will measure genital microbiota, genital cytokines, and BV, GUD, and genital epithelial disruption among 204 heterosexual couples over a one-year period. Study procedures include medical history, physical examination, collection of genital specimens, urine, and oral swabs, and HIV and STI testing. Evaluations and data collection will occur at Baseline and over 3 follow-up visits: 1 Month, 6 Months, 12 Months. After obtaining Informed Consent and Locator Information, the study procedures in order, are:

  1. HIV Counseling and testing
  2. Provision of urine and oral specimens
  3. Medical history and Physical Examination
  4. Obtaining of genital specimens (as part of Physical Exam)
  5. Computer assisted personal interview
  6. Dispensation of results of stat laboratory testing and any treatments (as needed)
Study Population: Sexually active Heterosexual couples with the men aged 18 – 35 years and the woman aged at least 16 years old and are residents of Kisumu, irrespective of HIV infection status.
Study Size:

A total of approximately 204 heterosexual couples will be enrolled.

Study Aims:

Aim 1: Determine how the penile microbiome leads to BV, GUD, and genital epithelial disruption.

Aim 2: Define factors causing variation in the penile microbiome over time and across men.

Aim 3: Map the linkage between the penile and vaginal microbiome, cytokines, and genital epithelial trauma to generate a model of the mechanism of epithelial disruption.
Exploratory Aim: Examine whether the association between penile bacteria and genitourinary outcomes in women is also correlated with the oral microbiome.