Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types

Abstract

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n=63) and non-infected (n=26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p<0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens ( Haemophilus , Stenotrophomonas , Acineobacter , Moraxella , Corynebacterium I , Gemella , Ralstonia , and Pseudomonas ) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. Further, we also assessed the microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.

Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

“…Importantly, we observed some opportunistic pathogens were associated with the progression of COVID-19, including nrMAGs from Klebsiella quasivariicola 41 , Klebsiella pneumoniae 42 , and Escherichia coli 43 . Related to our findings, multiple studies revealed high prevalence of bacterial pathogens in patients with COVID-19 17,59-62 , further supporting the possibility that secondary infections by opportunistic pathogens may affect the progression of COVID-19.…”

“…Importantly, we observed some opportunistic pathogens were associated with the progression of COVID-19, including nrMAGs from Klebsiella quasivariicola 41 , Klebsiella pneumoniae 42 , and Escherichia coli 43 . Related to our findings, multiple studies revealed high prevalence of bacterial pathogens in patients with COVID-19 17,[59][60][61][62] , further supporting the possibility that secondary infections by opportunistic pathogens may affect the progression of COVID-19. In particular, host gut microbiota provides colonization resistance against pathogens, for example, a previous study reported that mice treated with neomycin antibiotics were more susceptible than control mice to influenza viruses 63 .…”

Microbiota and compartment matter in the COVID-19 response

“…The reduction in microbiota diversity and beneficial commensals was associated with expansion of not only, in particular, Staphylococcus, but also Prevotella and Peptostreptococcus. Although only a few reports have assessed potential interactions between bacterial colonization of the upper airway and infection with SARS-CoV-2, this mirrors earlier reports of decreased microbiota diversity and Corynebacterium levels with a concurrent expansion of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acineobacter, Moraxella and Pseudomonas) in patients with COVID-19 8 . Through the integration of nasal bacteria with mucosal and plasma cytokines, a clearer picture starts to emerge for the complex interactions among host, virus and commensals that are associated with disease severity (Fig.…”

Nasopharyngeal Microbiome of COVID-19 Patients Using 16S Amplicon Analysis Revealed Distinct Bacterial Profile in Demised and Recovered Individuals

“…Although there was no signi cant difference in the different alpha diversity indices, we observed that the species richness was highest in the demised patient followed by recovers and control group. Previous studies have reported decrease in the microbial diversity in the COVID-19 patients [16,19]. Apart from dysbiosis in the nasopharyngeal microbiota due to SARS-COV-2 infection [18] also reported alteration in the oral and gut microbiota with respect to SARS-CoV-2 viral load in the COVID-19 patients.…”