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Small RNAs (sRNAs) are involved in the post-transcriptional regulation of metabolic pathways and in responses to stress and virulence. We analyzed the expression levels of five sRNAs of  Staphylococcus aureus  during human colonization or infection. Total RNA was isolated from nasal carriers, abscesses and cystic fibrosis patients (20 subjects per condition). The expression levels of the sRNAs were measured in the clinical samples and compared with those of the corresponding strains grown  in vitro . Five sRNAs were encoded and expressed in all clinical strains  in vitro .  In vivo , the global expression of the five sRNAs was extremely variable in the abscessed patients, more homogeneous in the cystic fibrosis patients, and highly uniform in the nasal carrier samples. The expression levels of the sRNAs  in vivo  resembled those obtained at exponential phase or late exponential phase of growth  in vitro , for three and one sRNA respectively; while for one sRNA, the expression was always higher  in vivo  as compared to  in vitro  growth. The  in vitro  conditions do not uniformly mimic the  in vivo  conditions for sRNA expression. Nasal colonization is associated with a unique expression pattern of sRNA that might reflect the commensalism of  S. aureus  in this niche.

The Expression of Small Regulatory RNAs in Clinical Samples Reflects the Different Life Styles of Staphylococcus aureus in Colonization vs. Infection