AEM:Several HIV+ women had distinct profiles dominated by E. coli.

Molecular definition of vaginal microbiota in East African commercial sex workers

ABSTRACT

Resistance to HIV infection in a cohort of commercial sex workers (CSW) living in Nairobi, Kenya is linked to mucosal and anti-inflammatory factors that may be influenced by vaginal microbiota. Since bacterial vaginosis (BV), a polymicrobial dysbiosis characterized by low levels of protective Lactobacillus organisms, is an established risk factor for HIV infection, we investigated whether vaginalmicrobiology was associated with HIV-exposed seronegative (HESN) or HIV-seropositive (HIV+) status in this cohort. A subset of 44 individuals was selected for deep sequencing analysis based on the chaperonin-60 universal target (cpn60 UT), including HESN (N=16), other HIV-seronegative controls (HIV-N, N=16) and HIV+ (N=12). Our findings indicate exceptionally high phylogenetic resolution of cpn60 UT using reads as short as 200bp, with 54 species in 29 genera detected in this group. Contrary to our initial hypothesis, few differences between HESN and HIV-N womenwere observed. Several HIV+ women had distinct profiles dominated by E. coli. Deep sequencing phylogenetic profile of vaginal microbiota corresponds closely to BV+/BV– diagnoses by microscopy, elucidating BV at the molecular level. A cluster of samples with intermediate abundance of Lactobacillusand dominant Gardnerella was identified, defining a distinct BV phenotype that may represent a transitional stage between BV+/BV–. Several α-/β-Proteobacteria, including the recently described Variovorax paradoxus, were found to correlate positivelywith increased Lactobacillus levels that define the BV– ("normal") phenotype. We conclude that cpn60 UT is ideally suited to next-generation sequencing technologies for further investigation of microbial community dynamics and mucosal immunity underlyingHIV resistance in this cohort.