Staphylococcus aureus superantigens (SAgs) are highly potent T cell mitogens. Antibodies against nonenterotoxin gene cluster (non-egc) SAgs are common in healthy adults, whereas neutralizing antibodies against egc SAgs are rare. We investigated the infecting S. aureus strains and the anti-SAg antibody response during S. aureus bacteremia (SAB). This prospective clinical study (www.clinicaltrials.gov, NCT00548002) included 43 injection drug users (IDUs) and 44 group-matched nonaddicts with SAB. spa genotypes and SAg gene patterns (multiplex PCR) of the S. aureus isolates were determined. The neutralizing capacities of sera obtained at the acute phase and the convalescent phase of SAB were tested against the SAg cocktail of the respective infecting strain and a panel of recombinant SAgs. The lineages CC59 and CC30 were more prevalent among bacteremia strains from IDUs than among strains from nonaddicts. SAg gene patterns in isolates from IDUs and nonaddicts were similar. At the acute phase of bacteremia, IDUs had more neutralizing antibodies against non-egc SAgs than did nonaddicts. Antibody titers frequently increased during infection. In contrast, there were no neutralizing antibodies against egc SAgs at disease onset and such antibodies were not induced by SAB. SAB triggers an antibody response only against non-egc SAgs. Preimmunization in IDU patients is probably due to previous exposure to the infecting strain.Staphylococcus aureus is a major human pathogen that causes a wide spectrum of infections, such as toxin-mediated diseases and systemic infections, for instance, bacteremia and endocarditis. At the same time, S. aureus is a commensal that colonizes approximately 35% of the healthy population in the nose (46,48).Among the numerous toxins of S. aureus are the 21 known staphylococcal superantigens (SAgs): the toxic shock syndrome toxin (TSST-1), the staphylococcal enterotoxins (SEA to SEE and SEG to SEJ), and the staphylococcal enterotoxin-like toxins (SElK to SElU) (13,24,33,35,38). They are encoded on mobile genetic elements, like phages and pathogenicity islands (25). SAgs are the causative agents of food poisoning and toxic shock syndrome, but their role in bacteremia is not well defined (13, 28). They can activate a large fraction of T lymphocytes by directly cross-linking certain T cell receptor V domains with conserved structures on major histocompatibility complex class II (MHC II) molecules. This results in a polyclonal T cell activation and massive cytokine release.The more recently described enterotoxin gene cluster (egc) harbors five or six SAg genes (seg, sei, selm, seln, selo, and sometimes selu), which cluster on a staphylococcal pathogenicity island (Sa) (17,23). In contrast to the non-egc SAgs, the egc is organized as an operon, and its genes are transcribed into a polycistronic mRNA (17). The egc genes are the most prevalent SAg genes in commensal and invasive S. aureus isolates, with frequencies ranging between 52 and 66% (4, 9, 14).