The present study reports differences in the nasopharyngeal microbial structure and composition of SARS-CoV-2-infected versus noninfected pregnant women. SARS-CoV-2-positive pregnant women showed differences in microbiota richness and evenness, with a higher relative abundance of Bacteroidetes (mainly due to the higher abundance of the Prevotellaceae family) and Tenericutes phyla. Additionally, we showed that these microbial changes were similar among women with past and present SARS-CoV-2 infection. No significant differences were reported in the most severe cases.
To our knowledge, this study is the first to describe the nasopharyngeal microbiota profile in SARS-CoV-2 infection during pregnancy. Previous studies in nonpregnant COVID-19 individuals reported a similar general microbial composition in the nasopharyngeal tract, with Firmicutes, Bacteroides, Proteobacteria and Actinobacteria as the most relevant phyla6,9. In the present study, a different nasopharyngeal profile was reported in pregnancies infected by SARS-CoV-2. Our findings are in agreement with several studies reporting differences in patients with this infection; however, the results are contradictory: Nardelli et al.10 reported differences in beta diversity, with a reduction in Proteobacteria and Fusobacteria phyla in a subsample of 18 COVID-19 patients. A significant reduction in alpha diversity was reported in 19 COVID-19 patients who were hospitalized in the ICU, whereas no changes were found due to SARS-CoV-2 positivity7. In contrast, Ventero et al.6 did not find any difference in the richness index between positive and negative cases; only in those patients who later developed more severe COVID-19 symptoms was there a loss of network complexity with a higher relative abundance of the Prevotella genus. No differences in bacterial richness, diversity or composition between positive and negative SARS-CoV-2 patients were reported by De Maio et al.9.
Such differences can be related to relatively small sample sizes, different populations and different severities of the condition, which requires several therapies.
Similar findings, such as a higher nasopharyngeal microbiota diversity and richness observed in SARS-CoV-2-infected pregnancies, have also been described in influenza-infected children compared to healthy children30. Other studies evaluating other viral infections, mostly influenza virus, have reported that the infection could change the diversity and composition of the nasopharyngeal bacterial community3,31. Moreover, in other parts of the respiratory tract, such as lung tissue, several authors reported an enrichment of pathogenic and commensal bacteria in COVID-19 patients32–35; in line with this, many authors agree that healthy lung tissue has a low density of microbial populations36, and disorders in the microbiota would be characterized by enrichment of OTUs35.
It can be hypothesized that respiratory microbial communities could play a role in SARS-CoV-2: infected patients had an altered respiratory tract microbiome with, in several cases, an increased abundance of OTUs. However, evidence is limited to studies with a relatively small sample size and different participant characteristics.
This is the first study reporting that changes in the nasopharyngeal microbial community persisted after SARS-CoV-2 infection in pregnant women. This evidence supports the idea of lost-lasting effects of these changes after the acute phase of the infection. Since we did not have a baseline evaluation, we cannot ascertain whether changes in the microbiota were present before the infection. However, we believe this is unlikely, considering that other respiratory infections have also been reported to induce changes in the nasopharyngeal microbiota3,30,31. An additional finding of this study was the association between taxa overrepresented in SARS-CoV-2-infected women and the levels of IgA/IgM, suggesting a potential relationship between the immune response and the microbiota37. Specifically, there was a negative association between IgA/IgM levels and the Corynebacterium genus, which is one of the main components of the nasopharyngeal microbiota38 and has been related to a healthy condition in several studies39 due to its potential capacity to compete with opportunistic pathogens40. These findings suggest that the microbiota alterations associated with SARS-CoV-2 could be mediated by the host immune system response.
In this study, we did not find any differences according to symptom severity. The small subgroup sample size and the high proportion of asymptomatic/mild infections may have hampered observing differences if these existed. Lee et al. reported in a nonpregnant population that several species from Alloprevotella and Prevotella were associated with influenza virus infection3. These taxa were also observed to be related to SARS-CoV-2 infection severity by Ventero et al.6. Moreover, overexpression of Prevotella proteins was related to an increase in the clinical severity of COVID-1933. In this study, we found a nonsignificant trend of higher relative abundance of the Prevotella genus and several groups from the Ruminococcaceae family.
Our study has some strengths and limitations that deserve comment. Among the strengths, to our knowledge, this is the first study of nasopharyngeal microbiota in pregnant women, providing data about this specific population and opening the door to future studies focused on them. Moreover, nasopharyngeal RT–PCR swab collection was always performed using a standardized procedure from trained medical staff at hospital admission, reducing potential bias before any treatment was started. Moreover, the population was very well characterized by SARS-CoV-2 infection status and COVID-19 symptoms. Specific positive and negative controls were introduced during sequencing to rule out potential contamination and bias due to the low microbial DNA samples. Despite these controls, we identified specific anaerobic gut microbes, such Ruminococcus and Faecalibacterium, in the nasopharynx samples, although in lower proportions. These bacteria have also been reported by other authors to be present in the nasopharynx41,42. Furthermore, the butyrate production of those microbial genera would be associated with a reduction in olfactory function42, which has been described as a COVID-19 symptom. Another potential explanation would be that the microbial database used as the curation of the open databases is critical for proper identification and reliable taxonomy assignment43.
Among limitations, the relatively small sample size did not allow us to draw robust conclusions from subgroup comparisons; additionally, as there were no data on the upper respiratory tract microbiota during pregnancy, it was not possible to discern if changes were due only to the pregnancy status itself and if this could be considered a protective effect for viral infections to become more severe. Finally, future studies are warranted to compare these data with women of the same age but in a nonpregnant status.