The bacterium Staphylococcus aureus is a major human pathogen for which the emergence of antibiotic resistance is a global public health concern. Infection severity, and in particular bacteraemia-associated mortality, has been attributed to several host-related factors, such as age and the presence of comorbidities. The role of the bacterium in infection severity is less well understood, as it is complicated by the multifaceted nature of bacterial virulence, which has so far prevented a robust mapping between genotype, phenotype and infection outcome. To investigate the role of bacterial factors in contributing to bacteraemia-associated mortality, we phenotyped a collection of sequenced clinical S. aureus isolates from patients with bloodstream infections, representing two globally important clonal types, CC22 and CC30. By adopting a genome-wide association study approach we identified and functionally verified several genetic loci that affect the expression of cytolytic toxicity and biofilm formation. By analysing the pooled data comprising bacterial genotype and phenotype together with clinical metadata within a machine-learning framework, we found significant clonal differences in the determinants most predictive of poor infection outcome. Whereas elevated cytolytic toxicity in combination with low levels of biofilm formation was predictive of an increased risk of mortality in infections by strains of a CC22 background, these virulence-specific factors had little influence on mortality rates associated with CC30 infections. Our results therefore suggest that different clones may have adopted different strategies to overcome host responses and cause severe pathology. Our study further demonstrates the use of a combined genomics and data analytic approach to enhance our understanding of bacterial pathogenesis at the individual level, which will be an important step towards personalized medicine and infectious disease management.
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Lowy, F. D. Staphylococcus aureus infections. N. Engl. J. Med. 339, 520–532 (1998).
Gordon, R. J. & Lowy, F. D. Pathogenesis of methicillin-resistant Staphylococcus aureus infection. Clin. Infect. Dis. 46, S350–S359 (2008).
Annual Epidemiological Commentary: Mandatory MRSA, MSSA and E. coli Bacteraemia and C. difficile Infection Data 2015/16 (Public Health England, 2016); https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/535635/AEC_final.pdf
Okon, K. O., Shittu, A. O., Kudi, A. A., Umar, H., Becker, K. & Schaumburg, F. Population dynamics of Staphylococcus aureus from northeastern Nigeria in 2007 and 2012. Epidemiol. Infect. 142, 1737–1740 (2014).
Walter, J., Haller, S., Blank, H. P., Eckmanns, T., Abu Sin, M. & Hermes, J. Incidence of invasive methicillin-resistant Staphylococcus aureus infections in Germany, 2010 to 2014. Euro. Surveill. https://dx.doi.org/10.2807/1560-7917.ES.2015.20.46.30067 (2015).
van Hal, S. J., Jenson, S. O., Vaska, V. L., Espedido, B. A., Pateron, D. L. & Gosbell, I. B. Predictors of mortality in Staphylococcus aureus bacteraemia. Clin. Microbiol. Rev. 25, 362–386 (2012).
Jenkins, A. et al. Differential expression and roles of Staphylococcus aureus virulence determinants during colonization and disease. mBio 6, e02272–14 (2015).
Crémieux, A. C. et al. α-Hemolysin, not Panton–Valentine leukocidin, impacts rabbit mortality from severe sepsis with methicillin-resistant Staphylococcus aureus osteomyelitis. J. Infect. Dis. 209, 1773–1780 (2014).
Sharma-Kuinkel, B. K. et al. Characterization of alpha-toxin hla gene variants, alpha-toxin expression levels, and levels of antibody to alpha-toxin in hemodialysis and postsurgical patients with Staphylococcus aureus bacteraemia. J. Clin. Microbiol. 53, 227–236 (2015).
Laabei, M. et al. Evolutionary trade-offs underlie the multi-faceted virulence of Staphylococcus aureus. PLoS Biol. 13, e1002229 (2015).
Rose, H. R. et al. Cytotoxic virulence predicts mortality in nosocomial pneumonia due to methicillin-resistant Staphylococcus aureus. J. Infect. Dis. 211, 1862–1874 (2015).
Das, S. et al. Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteraemia and abscess formation. Proc. Natl Acad. Sci. USA 113, E3101–E3110 (2016).
Cosgrove, S. E., Sakoulas, G., Perencevich, E. N., Schwaber, M. J., Karchmer, A. W. & Carmeli, Y. Comparison of mortality associated with methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteraemia: a meta-analysis. Clin. Infect. Dis. 36, 53–59 (2003).
Whitby, M., McLaws, M. L. & Berry, G. Risk of death from methicillin-resistant Staphylococcus aureus bacteraemia: a meta-analysis. Med. J. Aust. 175, 264–267 (2001).
Melzer, M., Eykyn, S. J., Gransden, W. R. & Chinn, S. Is methicillin- resistant Staphylococcus aureus more virulent than methicillin-susceptible S. aureus? A comparative cohort study of British patients with nosocomial infection and bacteraemia. Clin. Infect. Dis. 37, 1453–1460 (2003).
Laabei, M. et al. Predicting the virulence of MRSA from its genome sequence. Genome Res. 24, 839–849 (2014).
Rudkin, J. K. et al. Methicillin resistance reduces the virulence of healthcare-associated methicillin-resistant Staphylococcus aureus by interfering with the agr quorum sensing system. J. Infect. Dis. 205, 798–806 (2012).
Pozzi, C. et al. Methicillin resistance alters the biofilm phenotype and attenuates virulence in Staphylococcus aureus device-associated infections. PLoS Pathog. 8, e1002626 (2012).
Fey, P. D. et al. A genetic resource for rapid and comprehensive phenotype screening of nonessential Staphylococcus aureus genes. mBio 4, e00537-12 (2013).
Breiman, L. Random forests. Machine Learn. 45, 5–32 (2001).
Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).
Nilsson, I. M., Lee, J. C., Bremell, T., Rydén, C. & Tarkowski, A. The role of staphylococcal polysaccharide microcapsule expression in septicemia and septic arthritis. Infect. Immun. 65, 4216–4221 (1997).
Tzianabos, A. O., Wang, J. Y. & Lee, J. C. Structural rationale for the modulation of abscess formation by Staphylococcus aureus capsular polysaccharides. Proc. Natl Acad. Sci. USA 98, 9365–9370 (2001).
DeLeo, F. R. et al. Molecular differentiation of historic phage-type 80/81 and contemporary epidemic Staphylococcus aureus. Proc. Natl Acad. Sci. USA 108, 18091–18096 (2011).
Cheung, G. Y. et al. Production of an attenuated phenol-soluble modulin variant unique to the MRSA clonal complex 30 increases severity of bloodstream infection. PLoS Pathog. 10, e1004298 (2014).
Schweizer, M. L. et al. Increased mortality with accessory gene regulator (agr) dysfunction in Staphylococcus aureus among bacteremic patients. Antimicrob. Agents Chemother. 55, 1082–1087 (2011).
Murakami, H., Matsumaru, H., Kanamori, M., Hayashi, H. & Ohta, T. Cell wall-affecting antibiotics induce expression of a novel gene, drp35, in Staphylococcus aureus. Biochem. Biophys. Res. Commun. 264, 348–351 (1999).
Saunderson, R. B. et al. Impact of routine bedside infectious disease consultation on clinical management and outcome of Staphylococcus aureus bacteraemia in adults. Clin. Microbiol. Infect. 21, 779–785 (2015).
Charlson, M. E., Pompei, P., Ales, K. L. & MacKenzie, C. R. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J. Chronic Dis. 40, 373–383 (1987).
Lesens, O., Methlin, C. & Hansmann, Y. Role of comorbidity in mortality related to Staphylococcus aureus bacteraemia: a prospective study using the Charlson weighted index of comorbidity. Infect. Control Hosp. Epidemiol. 24, 890–896 (2003).
Köser, C. U. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267–2275 (2012).
Holden, M. T. et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 23, 653–664 (2013).
Holden, M. T. et al. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc. Natl Acad. Sci. USA 101, 9786–9791 (2004).
Ziebuhr, W., Krimmer, V., Rachid, S., Lossner, I., Gotz, F. & Hacker, J. A novel mechanism of phase variation of virulence in Staphylococcus epidermidis: evidence for control of the polysaccharide intercellular adhesin synthesis by alternating insertion and excision of the insertion sequence element IS256. Mol. Microbiol. 32, 345–356 (1999).
R Developement Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2011).
Genuer, R., Poggi, J.-M. & Tuleau-Malot, C. VSURF: An R Package for Variable Selection Using Random Forests. R J. 7, 19–33 (2015).
The authors thank T. Gouliouris, for his role in collecting and supplying the clinical data, and E. Nickerson and S. Aliyu for their role in the collection of clinical information. The authors also thank the Sanger Institute’s core Pathogen Production Groups and Pathogen Informatics Group.
M.R., M.L., M.S.T., R.B.S., B.B., M.E.T., S.J.P. and R.C.M. collected the data. M.R., M.L. and R.C.M. designed the experiments. M.L., K.O., E.S., M.Y., L.B., J.S., L.T. and G.M. performed experiments. M.R., M.L., M.S.T., S.R., S.B., S.J.P. and R.C.M. analysed the data. M.R., M.L., S.J.P. and R.C.M. wrote the manuscript.
The authors declare no competing financial interests.
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