Abstract
Microbiome disruption is a proposed mechanism for the observed differences in child health outcomes by maternal HIV status, but the early neonatal microbiome of HIV-exposed (HE) newborns is not well-studied. We used 16S ribosomal ribonucleic acid sequencing to analyze the microbiome composition of nasal, skin, and rectal samples collected ≤72 h after birth from 57 hospitalized neonates in Botswana, 33% of whom were HE. Beta diversity differed by anatomic compartment (P = .001) and days since birth; however, interindividual differences were greater than those by anatomic site (P = .001). There were not significant differences by maternal HIV status. When timing of maternal HIV diagnosis was accounted for, however, we noted statistically significant differences in beta diversity for nasal and skin swabs. Microbial composition of samples from neonates with mothers diagnosed with HIV prior to pregnancy were more similar to samples from HIV-unexposed than HE neonates with mothers diagnosed with HIV during this pregnancy (P = .03 and P < .01 in skin and nasal, respectively) suggesting that microbiome variations mediated by HIV exposure might only emerge later in infancy. In the entire cohort, we examined differences in relative taxa abundance of neonatal pathogens and other species of clinical interest. We noted differences by anatomic compartment, for example, increased Klebsiella pneumoniae in rectal samples and increased Acinetobacter baumannii in nasal samples, whereas other pathogens expected to differ by body site did not, for example, Enterococcus faecium and Streptococcus agalactiae, highlighting that in the early neonatal microbiome exposures may have a significant impact on microbiome development.