OC15.03: Differential nasopharyngeal microbiota profile of pregnant women with and without SARS‐CoV‐2 infection

Abstract

Nasopharyngeal microbiota has been implicated with respiratory infections; however, no previous evidence is reported during SARS-CoV-2 in pregnancy. The aim of this study was to characterise the nasopharyngeal microbiota in pregnant women with and without SARS-CoV-2 infection. Pregnant women from a multicentre prospective population-based cohort (March-June 2020 in Barcelona, Spain) in which the status of SARS-CoV-2 infection was known by a nasopharyngeal RT-PCR and antibodies in peripheral blood. DNA was extracted from nasopharyngeal swab samples, and the V3-V4 region of the 16S rRNA of bacteria was amplified using regions' specific primers. Differential abundance of taxa was tested, alpha and beta diversity were evaluated. Among 76 women, 38 were classified as positive and 38 for as negative for SARS-CoV-2 infection. All positive women were diagnosed by antibodies and 14 (37%) had also a positive RT-PCR. SARS-CoV-2 infection altered the overall composition of the nasopharyngeal microbiota (F=1.36, p = 0.001) with higher relative abundance of Tenericutes and Bacteroidetes phylum, as well as higher abundance of Prevotellaceae family. Infected women presented a different pattern of microbiota profiling due to beta diversity, and higher richness (Observed ASV<0.001) and evenness (Shannon index <0.001) at alpha diversity. These changes persisted after the acute infection revealed by a negative RT-PCR but positive antibodies, suggesting a long-lasting effect of SARS-CoV-2 in the nasopharyngeal microbiota. No significant differences were reported in mild vs. severe cases, suggesting a role of the SARS-CoV-2 infection itself but not on its severity. This is the first study on nasopharyngeal microbiota during pregnancy. SARS-CoV-2 infection altered the overall structure and diversity of the nasopharyngeal microbiota profiling and this effect seems to persist after the acute moment of the infection.