Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing

Abstract

Since December 2019, SARS-CoV-2 infection has been still rapidly spreading, resulting in a pandemic, followed by an increasing number of cases in countries throughout the world. The severity of the disease depends on the patient’s overall medical condition but no appropriate markers are available to establish the prognosis of the patients. We performed a 16S rRNA gene sequencing, revealing an altered composition of the nasal/oropharyngeal (NOP) microbiota in 21 patients affected by COVID-19, paucisymptomatic or in an Intensive Care Unit (ICU), as compared to 10 controls negative for COVID-19 or eight affected by a different Human Coronavirus (HKU, NL63 and OC43). A significant decrease in Chao1 index was observed when patients affected by COVID-19 (in ICU) were compared to paucisymptomatic. Furthermore, patients who were in ICU, paucisymptomatic or affected by other Coronaviruses all displayed a decrease in the Chao1 index when compared to controls, while Shannon index significantly decreased only in patients under ICU as compared to controls and paucisymptomatic patients. At the phylum level, Deinococcus-Thermus was present only in controls as compared to SARS-CoV-2 patients admitted to ICU, paucisymptomatic or affected by other coronaviruses. Candidatus Saccharibacteria (formerly known as TM7) was strongly increased in negative controls and SARS-CoV-2 paucisymptomatic patients as compared to SARS-CoV-2 ICU patients. Other modifications were observed at a lower taxonomy level. Complete depletion of Bifidobacterium and Clostridium was exclusively observed in ICU SARS-CoV-2 patients, which was the only group characterized by the presence of Salmonella, Scardovia, Serratia and Pectobacteriaceae. In conclusion, our preliminary results showed that nasal/oropharyngeal microbiota profiles of patients affected with SARS-CoV-2 may provide valuable information in order to facilitate the stratification of patients and may open the way to new interventional strategies in order to ameliorate the outcome of the patients.

Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose

“…However, a limited number of studies have examined the interplay between respiratory microbiome and acute SARS-CoV-2 infection. Studies of nasopharyngeal samples from small cohorts of mild and severe COVID-19 patients show variable differences in diversity and increased abundance of select phyla without accounting for the potential impact of viral load (Butler et al, 2021;De Maio et al, 2020;Nardelli et al, 2021;Rueca et al, 2021). Other studies of bronchoalveolar lavage and pharyngeal samples in severe patients reported a general dysbiosis of the lower respiratory microbiome similar to that of pneumonia patients (Budding et al, 2020;Shen et al, 2020).…”

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

“…Most of the nasal microbiome studies have been conducted on the influenza-infected patients or other respiratory diseases while less is known about the alteration of nasal microbiome during coronavirus infections. Recently, few studies have been conducted to understand the impact of SARS-CoV-2 infection and/or disease severity on the nasal and gut microbiome [ 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. Since SARS-CoV-2 infection is associated with the respiratory illness, hence it is imperative to have a better understanding about the nasal microbiome profile of the infected patients, as it is the first defensive line to avoid infection.…”

Related Factors to Streptococcus pneumoniae Invasive Infection and Clinical Manifestations: The Potential Role of Nasopharyngeal Microbiome

“…A very recent review about the role of respiratory microbiota in COVID-19 patients ( 95 ) concluded, based on previous evidence, that the dysbiosis in the microbiota in COVID-19 patients would potentially lead to infection or progression of the disease. However, studies on the characteristics of microbiome in COVID-19 patients are still scarce and conducted in a small number of patients to make them suitable for extrapolating conclusions ( 80 , 96 ).…”