The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens

Abstract

The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.

Viral strategies predisposing to respiratory bacterial superinfections

“…In the same study, asymptomatic carriers of influenza displayed a microbiome similar to healthy subjects, while, in symptomatic patients, respiratory pathogens, including S. pneumoniae , Haemophilus influenzae , Staphylococcus aureus , and Moraxella catarrhalis prevailed 104 . These data may suggest a possible role of microbiome in the clinical expression of influenza infection and also in the promotion of bacterial superinfections 105 . When evaluating the oropharyngeal microbiome composition of pneumonia patients with and without influenza A pH1N1 infection, no significant differences were found in common bacterial pneumonia‐causative agents (eg, Streptococcus species) 106 .…”

“…104 These data may suggest a possible role of microbiome in the clinical expression of influenza infection and also in the promotion of bacterial superinfections. 105 When evaluating the oropharyngeal microbiome composition of pneumonia patients with and without influenza A pH1N1 infection, no significant differences were found in common bacterial pneumonia-causative agents (eg, Streptococcus species). 106 However, a reduction of commensal bacteria diversity was detected in the pH1N1+ group, counterbalanced by a significant enrichment of Firmicutes and Proteobacteria.…”

SARS-CoV-2: fear versus data

“…Of course, the major flaw in this study is that the percentage of deaths attributable to the virus is not determined, but this is the case for all studies reporting respiratory virus infections, including SARS-CoV-2. Indeed, viral infections are ecosystem infections where the outcome depends on the inoculums and the surrounding microbiota [26]. Thus, certain bacteria seem to be associated with symptomatic manifestations, such as Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus, which are known to cause an excess of mortality due to secondary infection.…”

Influenza

“…Verschiedene Faktoren für die Prädisposition zur bakteriellen Folgeinfektion werden derzeit diskutiert, z. B. eine Deaktivierung ortsständiger Immunzellen und eine durch antivirale Zytokine bedingte Reduktion in der Diversität der lokalen mikrobiellen Standortflora mit Überwachsen von pathogenen Erregern [13,36]. Es ist anzunehmen, dass der Mehrzahl der ambulant erworbenen Pneumonien ("community-acquired pneumonia" [CAP]) ein viraler Trigger vorangeht, hierfür spricht sowohl die unerklärte Saisonalität der bakteriellen Pneumonie [47] als auch der häufige Polymerase-Kettenreaktions(PCR)-basierte Nachweis viraler respiratorischer Pathogene bei hospitalisierten CAP-Patienten [19].…”