Nasopharyngeal microflora affects the status and severity of SARS-CoV-2 infection

In a recent study posted on medRxiv* Preprint Server, Canadian researchers investigated how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection altered the composition of the microflora in the nasopharyngeal region of the host.

study: Changes in the nasopharyngeal microflora associated with SARS-CoV-2 infection status and disease severity.. Image Credit: Christoph Burgstedt / Shutterstock

Background

The risk and clinical outcome of SARS-CoV-2 infection varies widely from individual to individual. However, the underlying mechanism of these differences in the progression and etiology of coronavirus disease 2019 (COVID-19) is unknown. Studies show that the mucosal microbial flora affects the expression of host Toll-like receptors (TLRs) involved in virus detection. The study also showed a prevalence of bacterial co-infection in COVID-19 patients at 6.9%.

Similarly, elevated nasal cytokines are associated with adverse clinical outcomes in influenza patients. Therefore, investigating changes in the composition of the upper respiratory tract microflora after SARS-CoV-2 infection may be useful in assessing the effect on the severity of infection.

About research

In this study, researchers performed a nanopore full-length 16S ribosomal ribosomal (rRNA) sequence at 194. Nasopharyngeal swab Specimens collected between March 2020 and January 2022 from the general population of British Columbia, Canada. They consist of four HOSPOS COVID-19 patients, COMPOS COVID-19 patients, inpatient SARS-CoV-2 non-infected patients (HOSNEG), and non-infected community residents (COMNEG). I formed a research group.

A boxplot of relative abundance at the species level among the four study groups is displayed side by side.

In addition, the team performed sequence data analysis using the BugSeq16S analysis pipeline. They are SARS-CoV-2 envelope (E) and RNA-dependent RNA polymerase (RdRp) gene targets. They also used an in-house developed PCR-based assay to screen for SARS-CoV-2 mutants (VOCs), alpha, beta, gamma, delta, and omicrons in study samples. Finally, they used ALDEx2 to examine differences in the abundance of microbial taxa across the four research groups.

Survey results

The longer study period provided access to clinical specimens positive for a range of SARS-CoV-2 mutants. All study participants had a similar age distribution, but only 60.3% for men and 39.7% for women. The authors observed a tendency for Shannon / Simpson average diversity and uniformity to decrease in the COMPOS and COMNEG group samples. However, there was no significant alpha diversity among all study groups, as the results of the Kruskal-Wallis test with p-values ​​<0.05 show. In addition, the authors found some overlap in the 95% confidence ellipse among the four study groups. However, they differed in the composition of the microbial community and showed significant clustering at all three taxonomic ranks, species, genera, and family levels. Therefore, the p-values ​​for taxonomic ranks at the species, genus, and family levels were 0.009, 0.028, and 0.027, respectively.

In the SARS-CoV-2 infected group who were hospitalized and lived in the area, Acinetobacter When Moraxella Each was the most abundant genus. In both SARS-CoV-2 non-infected groups, Staphylococcus It was the most abundant genus on average. At the species level, the SARS-CoV-2 infected group had common nasal and opportunistic pathogens, including: Haemophilus influenzae, Staphylococcus haemolyticusWhen Staphylococcus aureus..In particular, inpatient groups infected with SARS-CoV-2 Klebsiella aerogenes As the most abundant species, as a higher average relative abundance Enterobacteriaceae More than any other research group.

Individuals infected with SARS-CoV-2 living in the area showed all discriminatory and abundant taxa, including families. Propionibacteriaceae, Neisseriaceae, Peptostreptococcales-Tissierellales,seed P. acnes P. acnesAnd genus Skin bacteria When Peptinophilus..

ALDEx2 is Streptococcus. When Corynebacterium Species in samples from SARS-CoV-2 infected individuals collected during the first three waves of the COVID-19 pandemic from March 2020 to May 2021. Viral load Or by SARS-CoV-2VOC type.

Conclusion

Overall, the study results showed detailed images of the differences between microbiota in individuals infected with SARS-CoV-2 and those not infected. Despite significant overlap of confidence ellipses, differences in nasopharyngeal microflora composition between study groups were relatively small.

Non-influenza respiratory virus infection increases host susceptibility Staphylococcus aureus A superinfection due to a decrease in the immune system’s ability to regulate clearance from the nasal passages. Therefore, with medical interventions such as intubation and exposure to antibiotics, Enterobacteriaceae Within a research group infected with SARS-CoV-2 during hospitalization.But the existence of Neisseriaceae The taxa of the SARS-CoV-2 infected groups living in the area remain unexplained.

Further research is needed to determine the functional characteristics of the nasopharyngeal microflora. This knowledge may help develop new COVID-19 prognostic markers and pave the way for new approaches to COVID-19 treatment.

*Important Notices

medRxiv Publish preliminary scientific reports that should not be considered definitive as they have not been peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.