Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants

We conducted a longitudinal analysis of a subset of 170 nasopharyngeal (NP) swabs of 20 infants and their mothers, identified from a sample library collected in Lusaka, Zambia between 2015 and 2016. The sample library was part of a nested time-series case comparator study within the prospective longitudinal Southern Africa Mother-Infant Pertussis study (SAMIPS). The samples belong to HIV-exposed (n=10) infants and their HIV+ mothers and HIV-uninfected healthy control (n=10) infants and their HIV- mothers, for a total of 20 infant subjects and 20 mother subjects. We matched the infants based on month of entry into study, mother's age, and mother's education. For each sample, we sequenced the V3-V4 region of the 16s rRNA gene and characterized the maturation microbiome over the first 14 weeks of life. We sought to determine what quantifiable differences exist between HIV-exposed and -unexposed infants, and what patterns are reflected in the mothers' NP microbiomes.