Potential Associations between Severity of Infection and the Presence of Virulence-Associated Genes in Clinical Strains of Staphylococcus aureus

et al. (2011) Potential Associations between Severity of Infection and the Presence of Virulence- Associated Genes in Clinical Strains of Staphylococcus aureus. PLoS ONE 6(4): e18673. doi:10.1371/journal.pone.0018673 Potential Associations between Severity of Infection and the Presence of Virulence-Associated Genes in Clinical Strains of Staphylococcus aureus Steven R. Gill 0 Lauren M. McIntyre 0 Charlotte L. Nelson 0 Brian Remortel 0 Tom Rude 0 L. Barth 0 Reller 0 Vance G. Fowler Jr. 0 Malcolm James Horsburgh, University of Liverpool, United Kingdom 0 1 Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America, 2 Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America, 3 NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York, United States of America , 4 Molecular Genetics and Microbiology , University of Florida, Gainesville, Florida, United States of America, 5 Duke Clinical Research Institute, Duke University Medical Center , Durham , North Carolina, United States of America, 6 J. Craig Venter Institute, Rockville, Maryland, United States of America, 7 Division of Infectious Diseases, Department of Medicine, Duke University Medical Center , Durham , North Carolina, United States of America, 8 Clinical Microbiology Laboratory, Duke University Medical Center , Durham, North Carolina , United States of America Background: The clinical spectrum of Staphylococcus aureus infection ranges from asymptomatic nasal carriage to osteomyelitis, infective endocarditis (IE) and death. In this study, we evaluate potential association between the presence of specific genes in a collection of prospectively characterized S. aureus clinical isolates and clinical outcome. Methodology/Principal Findings: Two hundred thirty-nine S. aureus isolates (121 methicillin-resistant S. aureus [MRSA] and 118 methicillin-susceptible S. aureus [MSSA]) were screened by array comparative genomic hybridization (aCGH) to identify genes implicated in complicated infections. After adjustment for multiple tests, 226 genes were significantly associated with severity of infection. Of these 226 genes, 185 were not in the SCCmec element. Within the 185 non-SCCmec genes, 171 were less common and 14 more common in the complicated infection group. Among the 41 genes in the SCCmec element, 37 were more common and 4 were less common in the complicated group. A total of 51 of the 2014 sequences evaluated, 14 non-SCCmec and 37 SCCmec, were identified as genes of interest. Conclusions/Significance: Of the 171 genes less common in complicated infections, 152 are of unknown function and may contribute to attenuation of virulence. The 14 non-SCCmec genes more common in complicated infections include bacteriophage-encoded genes such as regulatory factors and autolysins with potential roles in tissue adhesion or biofilm formation. - Funding: This work was supported by funds from National Institutes of Health (NIH) (R01-AI059111 and R01-AI068804). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Dr. Fowler has served as a consultant for Astellas, Cubist, Inhibitex, Merck, Johnson & Johnson, Shire, Leo Pharmaceuticals, NovaDigm, The Medicines Company, Baxter Pharmaceuticals & Biosynexus; has received grant or research support from Astellas, Cubist, Inhibitex, Merck, Theravance, Cerexa, Pfizer, Novartis, Advanced Liquid Logic and National Institute of Health; has received honoraria from Arpida, Astellas, Cubist, Inhibitex, Merck, Pfizer, Targanta, Theravance, Wyeth, Ortho-McNeil, Novartis & Vertex Pharmaceuticals; has served on an advisory committee for Cubist; is employed by Duke University; and has served as a speakers bureau for Cubist. The clinical spectrum of Staphylococcus aureus is diverse, ranging from asymptomatic colonization to osteoarticular infections, endocarditis, and death [1,2,3,4,5,6]. Although a growing body of evidence suggests that bacterial genetic characteristics may be associated with distinct clinical manifestations of S. aureus [7,8,9,10,11,12,13], the association between S. aureus genes and severity of illness is incompletely understood. Using multi-locus sequence typing (MLST), we previously demonstrated a significant association between specific clonal complexes (CC) and severity of infection in S. aureus [9]. Among 371 clinically well-characterized S. aureus from diverse clinical settings, we showed that CC5 and CC30 were significantly associated with hematogenous complications of S. aureus such as endocarditis, septic arthritis, and vertebral osteomyelitis. Isolates within these CCs were also implicated using staphylococcal protein A (spa) [14] and staphylococcal cassette chromosome mec (SCCmec) typing [15]. However, the genetic basis for these associations is unknown. The current investigation seeks to evaluate potential associations between the presence of specific genes and clinical outcome. To do this, we used a novel array comparative genome hybridization (aCGH) analysis method to identify individual genes in a large collection of clinically well-characterized S. aureus isolates from a wide range of infection severity [16]. We hypothesized that the association between CC5 and CC30 and hematogenous complications was due to the presence of specific bacterial genes contained within these clonal backgrounds, and tested this hypothesis for over 2,000 genes in the genomes of 239 clinical S. aureus isolates. Subject characteristics This study was approved by the Duke University Medical Center (DUMC) Institutional Review Board. Written informed consent was obtained from all participants involved in this study. At Duke Medical Center, hospitalized adult patients with at least one blood culture positive for S. aureus were prospectively identified between September 1994 and October 2003 [17]. Bacterial bloodstream isolates were cataloged, stored and corresponding clinical data were prospectively collected [17]. Twelve weeks after initial positive blood culture, clinical outcomes were prospectively assessed. Patients were excluded from the investigation for the following reasons: outpatient status, age ,18 years, polymicrobial infection, neutropenia (absolute neutrophil count ,1.06109/liter), death before evaluation by the investigators, injection drug use, surgery within 30 days, or indwelling prostheses. These exclusion criteria eliminate important non-pathogen characteristics that can influence the severity of staphylococcal disease. Next, we used strict definitions to identify three phenotypically distinct clinical groups which represent a progression from healthy individuals to those who are severely affected: 1) nasal carriage, 2) uncomplicated infection, and 3) bacteremia with hematogenous complications. Nasal carriage isolates were obtained from the (...truncated)