Within-host evolution of longitudinal Staphylococcus aureus isolates from a severe chronic rhinosinusitis patient reveals chronic colonisation with a change towards a mucoid phenotype

Chronic Rhinosinusitis (CRS) is a common long-standing inflammation of the nasal and paranasal sinus mucosa, of which the underlying cause remains unclear. Nevertheless, studies indicate that Staphylococcus aureus, particularly in biofilm formations, may contribute to the severity of the condition. The mucoid phenotype of S. aureus, known for its enhanced ability to form biofilms, has been linked to a 5-base pair deletion upstream of the icaABCD operon. This deletion increases the production of polysaccharide intercellular adhesin (PIA), a primary component of S. aureus biofilm extracellular polymeric substance.In this study, we harvested 8 sequential longitudinal isolates from the sinonasal cavity of a severe CRS patient over 672 days (T1-T8). We characterized them using microbiology assays, short and long-read sequencing to assemble near-perfect complete circular genomes and Liquid Chromatography-Mass Spectrometry (LC-MS) of biofilm-secreted exoproteins.Our results indicate chronic colonization with the same strain over time with the acquisition of an insertion sequence belonging to the IS21 family in the icaR-icaABCD operon, leading to the truncation of the ica repressor gene (icaR) and point mutations in the mfd, isdA, and ymdB genes. LC-MS analysis of biofilm exoproteins revealed a significant increase in secreted enterotoxin proteins such as Seg, Sei, Sen, Seo, and Seu (pIn conclusion, we have characterized the within-host evolution of S. aureus of a severe CRS patient towards a mucoid hyperbiofilm-forming phenotype with increased secretion of virulence factors. This might provide a survival advantage for the bacterial strain in vivo.