Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients

Abstract

We investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed significant microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection samples already collected for SARS-CoV-2 testing (viral transport media) and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.

Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment

“…Propionibacteriaceae, or Corynebacteriam accolens, as was reported for a study of 50 patients (n = 40 positive, 10 negative) in Baltimore [3]. Another study found no differences in the nasopharyngeal microbiota of patients who had mild COVID-19 (n = 9 positive, 10 negative) [2]. Analysis of patient samples in Nashville (n = 38 mild to moderate positive, 21 negative) revealed the complexity of interaction between viruses and bacteria in the upper respiratory tract, as differences in the airway microbiome were reported to be dependent on the SARS-CoV-2 viral load [16].…”

“…The samples were nasopharyngeal swabs in viral transport media (VTM) collected under IRB-approved protocol 2019.334 along with metadata in 3-8 April 2020 in Louisiana, USA. The utility of this type of medical waste sample for microbiome studies has been previously established for Influenza [19] and SARS-CoV-2 [2,20]. Demographics associated with the samples are presented in Table 1 and are representative of the demographic breakdown of testing at the time.…”

“…Although much research has been rapidly produced regarding the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, only a handful of studies have examined associations of viral infection with the nasopharyngeal (NP) microbiome [1][2][3][4][5]. It is hypothesized that SARS-CoV-2 infection may compromise immunity and increase bacterial attachment, growth, and possibly lead to co-infections or "super infections" [5,6].…”

“…Studies of the NP microbiome in SARS-CoV-2 positive and negative samples have found a range of observations; from no differences in those with mild COVID-19 to species-specific alterations that differed in reports from different cities and patient populations [2][3][4]16,17]. In one study of co-infections in the respiratory tract (n = 100 positive) that found limited viral genetic variation among patients, the authors suggested that the presence of particular species (e.g., Clostridium botulinum, Bacillus cereus and Halomonas spp.)…”

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

“…Braun et al [37] (n=33), De Maio et al [38] (n=40), and Liu et al [39] (n=9) showed no significant differences in the nasopharyngeal microbial community between COVID-19 and control patients using α-β diversity and taxonomic compositional analysis. Whereas Mostafa et al [40] (n=50) and Engen et al [41] (n=19) reported a lower α diversity (Chao1, Shannon, and Simpson indexes) in COVID-19 compared to healthy patients, and both groups showed significant dissimilarities in β diversity. Therefore, there is controversy regarding lung and nasopharyngeal microbiota composition on SARS-CoV2 infection.…”