Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Article https://doi.org/10.1038/s41467-023-37200-w Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria Received: 1 February 2023 A list of authors and their affiliations appears at the end of the paper. 1234567890():,; 1234567890():,; Accepted: 6 March 2023 Check for updates Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research. Previously under-recognised, sepsis has only recently become part of the Global Burden of Disease register. Estimated at ~50 million cases with ~11 million deaths in 20171, the World Health Organization (WHO) attributes ~20% of human mortality to sepsis worldwide (https://www. cidrap.umn.edu/news-perspective/2020/09/who-says-sepsis-causes20-global-deaths), with disease burden borne disproportionately by developing countries (~85%)2. Even in developed nations, sepsis causes between one-third and one-half of all in-hospital deaths3,4, killing more people than heart attacks, stroke, or cancers of the prostate, breast or colon5. Sepsis (infection-associated organ failure)2 represents the end stage of an illness continuum and is probably three times more common and at least twice as lethal as previously thought3,4. In sepsis survivors, severe physical, cognitive, and psychological sequelae may persist for decades6. Among 5,033,257 severe sepsis hospitalisations in the U.S. between 1999 and 2008, 38.5% of cases reported a causative pathogen, with Gram-negative bacteria predominating (51.5%), followed by Gram-positive bacteria (45.6%), anaerobes (1.7%), and fungi (1.2%)7. Escherichia coli is responsible for approximately one-quarter of all episodes of blood-stream infections (bacteremia) and ~50% of all Gram-negative bacteremias8. The 30-day all-cause mortality rate of E. coli bloodstream infection is ~16% and is significantly higher when associated with resistance to extended-spectrum β-lactam antibiotics9. Approximately half of all E. coli bloodstream infections originate from urinary tract infections, with gastrointestinal foci also common10. The majority of E. coli bloodstream infections are caused by a small group of high-risk globally dominant clones, with sequence type 131 (ST131) being one of the most common2,11,12. Taxonomically diverse Klebsiella pneumoniae species complex (KpSC) is a closely related set of species that are a major cause of community-acquired and nosocomial Gramnegative bloodstream infections often characterised by high-level antimicrobial resistance (AMR). Many KpSC (K. pneumoniae, K. quasipneumoniae subsp. similipneumoniae, K. quasipneumoniae subsp. quasipneumoniae, K. variicola subsp. tropica, K. variicola subsp. variicola, K. quasivariicola, and K. africana) with mucoid colony phenotypes due to encapsulation by secreted polysaccharides and at least one iron acquisition system are hyperinvasive and associated with sepsis13. KpSC bloodstream infections occur in ~1/10,000 individuals per year, with a case fatality rate of ~20% that varies with the setting, age group and co-morbidities8,14. Staphylococcus aureus is both a commensal and an opportunistic Gram-positive human pathogen with multiple mechanisms for e-mail: Nature Communications | (2023)14:1530 1 Article evading the host immune response and infecting diverse tissue sites. With more than 10 cases/100,000 population/year and associated mortality of up to 20%15–17, invasive S. aureus infections have major societal and economic impacts with estimated costs exceeding $2.2 billion annually in the US alone18. Streptococcus pyogenes is another Gram-positive bacterial pathogen causing severe disease including bloodstream infections, necrotising fasciitis, and puerperal sepsis in pregnant or post-partum women, altogether resulting in 660,000 cases and 160,000 deaths worldwide each year19,20. During invasive or bloodstream infection, S. aureus and S. pyogenes expression of superantigen toxins can lead to toxic shock syndrome and worsening sepsis15,19. Once triggered, a cascade of host responses drives sepsis and early critical care interventions to support organ system function and clear the causative pathogens is essential to patient survival. Among the different types of sepsis, only bacterial infection has clear evidence for time-critical mortality benefits from targeted antibiotic therapy, and these data form the basis for the current international consensus standard of care21. However, the detection of the presence and antibiotic susceptibility of a pathogen may be insufficient, since increasing evidence suggests that clinical interventions are best guided by the presence or absence of specific virulence factors22. While important genetic determinants not evident in standard test conditions are being discovered in prominent pathogens, high-quality baseline physiological data will be essential to facilitate the future discovery of pathogendirected diagnostics for sepsis23. To model the impact of transition into the human bloodstream during sepsis, we have undertaken a systematic comparison of global responses in representative leading human sepsis pathogens—comparing their growth in a tissue-model medium (RPMI) versus human serum, using integrated genomic, transcriptomic, proteomic and metabolomic methodologies (Fig. 1). This cross-species comparative investigation of multiple clinical sepsis isolates provides a compendium of both conserved and pathogenspecific responses that may provide targets for future therapeutic intervention. Fig. 1 | Schematic of the experimental workflow employed in this study. A sample of gDNA extracted from each strain of each species was split in order to prepare parallel sequencing libraries for both long-read (PacBio RSII) and shortread (Illumina MiSeq) sequencing. Biological replicates for transcriptomics, Nature Communications | (2023)14:1530 https://doi.org/10.1038/s41467-023-37200-w Results and discussion Genome analysis The human sepsis pathogens investigated in this study and their clinical features of interest are listed in Tab (...truncated)