Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients

Abstract

While populations at risk for severe SARS-CoV-2 infections have been clearly identified, susceptibility to the infection and its clinical course remain unpredictable. As the nasopharyngeal microbiota may promote the acquisition of several respiratory infections and have an impact on the evolution of their outcome, we studied the nasopharyngeal microbiota of COVID-19 patients in association with baseline disease-related clinical features compared to that of patients tested negative. We retrospectively analyzed 120 nasopharyngeal pseudonymized samples, obtained for diagnosis, divided into groups (infected patients with a favorable outcome, asymptomatic, and deceased patients) and patients tested negative for SARS-CoV-2, by using Illumina-16S ribosomal ribonucleic acid (rRNA) sequencing and specific polymerase chain reaction (PCR) targeting pathogens. We first found a depletion of anaerobes among COVID-19 patients, irrespective of the clinical presentation of the infection (p < 0.029). We detected 9 taxa discriminating patients tested positive for SARS-CoV-2 from those that were negative including Corynebacterium propinquum/pseudodiphtericum (p ≤ 0.05), Moraxella catarrhalis (p ≤ 0.05), Bacillus massiliamazoniensis (p ≤ 0.01), Anaerobacillus alkalidiazotrophicus (p ≤ 0.05), Staphylococcus capitis subsp. capitis (p ≤ 0.001), and Afipia birgiae (p ≤ 0.001) with 16S rRNA sequencing, and Streptococcus pneumoniae (p ≤ 0.01), Klebsiella pneumoniae (p ≤ 0.01), and Enterococcus faecalis (p ≤ 0.05) using real-time PCR. By designing a specific real-time PCR, we also demonstrated that C. propinquum is decreased in asymptomatic individuals compared to other SARS-CoV 2 positive patients. These findings indicate that the nasopharyngeal microbiota as in any respiratory infection plays a role in the clinical course of the disease. Further studies are needed to elucidate the potential role in the clinical course of the disease of M. catarrhalis, Corynebacterium accolens, and more specifically Corynebacterium propinquum/diphteriticum in order to include them as predictors of the severity of COVID-19.

Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors

“…SARS-CoV-2 replication initiates in the URT and continues in the alveoli of the lungs influencing the local immunological environment. This causes characteristic alterations in the diversity and composition of the microbiota in the oral cavity [ 599 , 600 ] and the upper [ 426 , 601 ] and lower respiratory tract (LRT) [ 602 , 603 ]. The diversity of the microbiota typically increases in the URT [ 604 , 605 , 606 ] due to the emergence of opportunistic pathogens ( Klebsiella , Streptococcus , Veillonella , Prevotella , Enterococcus , Rothia , etc.).…”

The nasopharyngeal microbiome in COVID-19

“…On the other hand, consistent with these results, the work by Bai and colleagues, which included 37 critically ill COVID-19 patients and 20 uninfected controls, showed a reduction in commensal bacteria and higher abundance of pathogenic bacteria in patients compared to healthy uninfected controls (Table S1) [ 52 ]. But even more interesting are the approaches analyzing the nasopharyngeal microbiota composition of COVID-19 patients with different levels of disease severity within the same study, since most of these works observed significant differences when comparing symptomatic subjects to asymptomatic/paucisymptomatic individuals and/or uninfected controls (Table S1) [ 46 , 50 , 54-56 , 64-66 , 68-70 ]. Among the studies belonging to this group, Nardelli and colleagues, who were the first authors to select a homogeneous group of COVID-19 patients sharing that all of them were symptomatic, revealed that Proteobacteria and Fusobacteria relative abundances decreased in symptomatic COVID-19 patients compared to uninfected controls, particularly the genera Leptotrichia , Haemophilus , and Fusobacterium (Table S1) [ 46 ].…”

“…Interestingly, contradictory results regarding the abundance of the genus Corynebacterium in the nasopharynx of COVID-19 patients associated to the severity of their disease have been reported. While some studies suggest an association between its increased abundance or its prevalence in the nasopharynx and a more severe disease [ 60 , 68 ], others observed that the genus Corynebacterium was less abundant in SARS-CoV-2 positive subjects compared to uninfected controls [ 49 ], or that its abundance decreased as the severity of the COVID-19 disease was higher (Table S1) [ 65 , 69 ]. Thus, besides the previously mentioned results showing that Corynebacterium , together with Staphylococcus , dominates the nasopharyngeal microbiota of severe COVID-19 patients who were admitted to the intensive care unit [ 60 ], Tchoupou Saha and colleagues also detected that the relative abundance of a member of the Corynebacterium genus, C. propinquum , was increased in symptomatic COVID-19 patients compared to asymptomatic (Table S1) [ 68 ].…”

“…While some studies suggest an association between its increased abundance or its prevalence in the nasopharynx and a more severe disease [ 60 , 68 ], others observed that the genus Corynebacterium was less abundant in SARS-CoV-2 positive subjects compared to uninfected controls [ 49 ], or that its abundance decreased as the severity of the COVID-19 disease was higher (Table S1) [ 65 , 69 ]. Thus, besides the previously mentioned results showing that Corynebacterium , together with Staphylococcus , dominates the nasopharyngeal microbiota of severe COVID-19 patients who were admitted to the intensive care unit [ 60 ], Tchoupou Saha and colleagues also detected that the relative abundance of a member of the Corynebacterium genus, C. propinquum , was increased in symptomatic COVID-19 patients compared to asymptomatic (Table S1) [ 68 ]. On the contrary, a study by Shilts and colleagues, which included 20 uninfected controls and 83 SARS-CoV-2 positive subjects with different COVID-19 severities, ranging from asymptomatic to very severe cases, found that changes in the nasopharyngeal microbiota were associated to the disease severity, and in particular, Corynebacterium clearly decreased as COVID-19 severity increased (Table S1) [ 65 ].…”

High abundance of butyrate-producing bacteria in the naso-oropharynx of SARS-CoV-2-infected persons in an African population: implications for low disease severity

“…Similarly, studies conducted elsewhere found that Firmicutes and other butyrate producers, such as Fusobacterium, were decreased in asymptomatic persons compared to those with severe disease outcomes (43) and in con rmed COVID-19 cases (12,39).…”