The Staphylococcus aureus secretome - TI Pharma

Proteogenomics uncovers extreme heterogeneity in the Staphylococcus aureus
exoproteome due to genomic plasticity and variant gene regulation
Introduction
Staphylococcus aureus causes a wide variety of human infections ranging from superficial
lesions to severe systemic diseases. Up to one third of the human population carries S. aureus
as a commensal bacterium without developing any clinical symptoms. Nevertheless, the
colonizing strain can serve as an endogenous reservoir for infection, the incidence of
bacteremia being less than 0.02% (von Eiff et al., 2001). Individuals colonized with S. aureus
have thus a higher risk to develop an S. aureus infection, but they are also more likely to
overcome the disease (Wertheim et al., 2004). It is undisputed that the incidence and outcome
of invasive staphylococcal diseases strongly depend on host factors, in particular the immune
status of a patient. Yet, the species S. aureus is highly diverse and up to 30% of the genomes
of different isolates consist of variable regions, such as pathogenicity islands, lysogenic
bacteriophages, and plasmids (Witney et al., 2005). Since these genetic elements encode the
majority of virulence factors, it is generally thought that their presence critically determines
the clinical symptoms and outcome of an S. aureus infection. However, virulence-associated
genes may also be located in the core genome as illustrated by the spa, aur, hla, lip, clfAB,
map/eap, fnbA, and coa genes (Holden et al., 2004; Peacock et al., 2002). It is generally
accepted that certain strains are more virulent than others (Melles et al., 2004), although,
under certain conditions, any S. aureus genotype may have the potential to induce lifethreatening
infections. This suggests that there is no simple relationship between bacterial
genotype and clinical outcome. Apart from several well-defined toxin-mediated diseases (e.g.
toxic shock and scalded skin syndrome, necrotizing pneumonia) (Musser et al., 1990;
Gemmell, 1995; Labandeira-Rey et al., 2007), it remains difficult to predict the onset and
course of an S. aureus infection in a given patient solely on the basis of the virulence gene
repertoire of the strain involved. In fact, the vast majority of severe S. aureus infections are
probably caused by the concerted action of multiple virulence factors. Molecular typing and
genome analyses of clinical isolates focussing on virulence gene distribution have been major
steps towards a thorough understanding of these complex phenomena. Also, there is growing
evidence that the presence and activities of certain regulators play a role in the variation of
virulence gene expression in clinical isolates (Blevins et al., 2002; Karlsson and Arvidson,
2002).
Here, we complement the genetic identification of virulence factors in different S. aureus
isolates with proteome analyses of secreted proteins, which represent an important reservoir
of virulence factors. More specifically, in this proteogenomics approach we have addressed
the questions (i) of whether particular virulence genes are expressed in different isolates and,
if so, (ii) in what quantities? The results reveal an unprecedented heterogeneity in the
analyzed S. aureus exoproteomes, which is caused by both genomic plasticity and an amazing
variability in the levels of gene expression.
Materials and Methods
Bacterial strains
Twenty five S. aureus isolates derived from a variety of human infections were collected by the
university hospital in Groningen. All strains were identified as S. aureus by plating and coagulase tests.
Resistance against antibiotics was determined by routine disk diffusion assays. For RNAIII
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