Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus

<b>Introduction.</b> <i>Staphylococcus aureus</i> is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that <i>S. aureus</i> can colonize more the pharynx than the nose. In addition, <i>S. aureus</i> can persist in these sites for prolonged periods of time.<b>Hypothesis.</b> The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of <i>S. aureus</i>.<b>Aim.</b> Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of <i>S. aureus</i>.<b>Methodology.</b> <i>S. aureus</i> carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.<b>Results.</b> A greater colonization of <i>S. aureus</i> was found in the pharynx than in the nose. The microbiomes of <i>S. aureus</i> carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus <i>Staphylococcus</i> in pharyngeal and nasal <i>S. aureus</i> carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of <i>Staphylococcus</i>-associated pathways in the nose than in the pharynx.<b>Conclusion.</b> <i>S. aureus</i> can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of <i>S. aureus</i>, but the pharyngeal and nasal microbiomes are different independent of the type of <i>S. aureus</i> carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of <i>S. aureus</i>.