Enrollment and sample collection

Subjects were enrolled at two collection sites in Yaounde and samples collected were transferred to the International Research Centre for HIV/AIDS Management and Prevention, Chantal Biya’s, Yaounde. Our control group (HIV uninfected as determined by negative ELISA assay) were screened at the entry point at the Pediatric Units at our collection sites. In the HIV-infected cohort, all infected children were on prophylactic co-trimoxazole as from 6 weeks of age, and on ART once diagnosis was confirmed according to the protocol of National guidelines on the prevention and management of HIV in Cameroon. 74 of them were on the NNRTIs: ABC+3TC+EFV (20 participants), ABC+3TC+NVP (20 participants), TDF+3TC+EFV (19 participants), AZT+3TC+EFV (8 participants), and ABC+3TC+NVP (7 participants). All the 13 PIs participants were on the molecules ABC+3TC+LPV/r.

The specifics of the cohort attributes can be found in Table ​Table1.1. None of the participants were taking antibiotics or antifungal other than the prescribed prophylactic co-trimoxazole at the time of recruitment or within the past 4 weeks prior to sample collection. Socio-demographic and clinical data were collected using a questionnaire.

Fecal samples were collected in a dry, sterile stool container and children who were unable to provide stool the same day were advised on how to collect stool in the provided container and bring them the next day. Samples were transported to the laboratory within 30 min of collection in a cooler box and immediately placed at − 30 °C. Blood samples were collected by venipuncture at the collection sites and transported to the Medical Analyses Laboratory, International Research Centre for HIV/AIDS Management and Prevention, Chantal Biya’s, Yaounde for analysis.