Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda

Abstract

Background The global burden of sepsis is concentrated in sub-Saharan Africa, where severe infections disproportionately affect young, HIV-infected adults and high-burden pathogens are unique. In this context, poor understanding of sepsis immunopathology represents a crucial barrier to development of locally-effective treatment strategies. We sought to determine inter-individual immunologic heterogeneity among adults hospitalized with sepsis in a sub-Saharan African setting, and characterize associations between immune subtypes, infecting pathogens, and clinical outcomes. Methods Among a prospective observational cohort of 288 adults hospitalized with suspected sepsis in Uganda, we applied machine learning methods to 14 soluble host immune mediators, reflective of key domains of sepsis immunopathology (innate and adaptive immune activation, endothelial dysfunction, fibrinolysis), to identify immune subtypes in randomly-split discovery (N = 201) and internal validation (N = 87) sub-cohorts. In parallel, we applied similar methods to whole-blood RNA-sequencing data from a consecutive subset of patients (N = 128) to identify transcriptional subtypes, which we characterized using biological pathway and immune cell-type deconvolution analyses. Results Unsupervised clustering consistently identified two immune subtypes defined by differential activation of pro-inflammatory innate and adaptive immune pathways, with transcriptional evidence of concomitant CD56(-)/CD16( +) NK-cell expansion, T-cell exhaustion, and oxidative-stress and hypoxia-induced metabolic and cell-cycle reprogramming in the hyperinflammatory subtype. Immune subtypes defined by greater pro-inflammatory immune activation, T-cell exhaustion, and metabolic reprogramming were consistently associated with a high-prevalence of severe and often disseminated HIV-associated tuberculosis, as well as more extensive organ dysfunction, worse functional outcomes, and higher 30-day mortality. Conclusions Our results highlight unique host- and pathogen-driven features of sepsis immunopathology in sub-Saharan Africa, including the importance of severe HIV-associated tuberculosis, and reinforce the need to develop more biologically-informed treatment strategies in the region, particularly those incorporating immunomodulation.

HIV infection drives pro-inflammatory immunothrombotic pathway activation and organ dysfunction among adults with sepsis in Uganda

“…Secondary outcomes included a composite measure of in-hospital outcome (death in-hospital or transfer to Uganda's national referral hospital due to progressive severity of illness) and functional status at discharge (among patients who survived and were not transferred). Further details of the RESERVE-U study and study site capacity have been published and are summarized in the supplement [8,9]. Among adults enrolled in the RESERVE-U study, we first determined the impact of HIV on infecting pathogens, organ dysfunction, and in-hospital and 30day outcomes.…”

Performance of the Universal Vital Assessment (UVA) mortality risk score in hospitalized adults with infection in Rwanda: A retrospective external validation study

“…After successful prospective validation, both the UVA score and the amalgamated qSOFA could be used clinically to identify patients at risk for in-hospital death, which could be evaluated in a cluster randomized trial to determine whether identification of mortality risk leads to improved outcomes in different clinical settings. The UVA score has been used by others to control for severity of illness at admission in observational clinical studies and it could also be used for risk stratification in interventional studies [ 14 , 15 ]. For example, since steroid therapy for COVID-19 is based on severity of illness, the UVA score might be a useful indicator for steroid therapy in resource limited settings, which would need to be tested prospectively.…”

Brief Report: Detection of Urine Lipoarabinomannan Is Associated With Proinflammatory Innate Immune Activation, Impaired Host Defense, and Organ Dysfunction in Adults With Severe HIV-Associated Tuberculosis in Uganda

“…In serum samples collected at RESERVE-U enrollment, we quantitated, using Luminex immunoassays (Luminex, Austin, TX), 14 soluble immune mediators reflective of immunopathological domains that may contribute to infection-related organ dysfunction, including among patients with severe HIV/TB. 3,13,[15][16][17][18] ). From whole-blood samples collected in PAXgene blood RNA tubes from a consecutive subset of patients, RNA was isolated and purified using PAXgene blood RNA kits (Qiagen, Hilden, Germany), after which RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (NEB, Ipswich, MA).…”

“…13,14 Patients were included in the parent RESERVE-U study if they fulfilled the following criteria: (1) age $18 years, (2) reported a history of fever or had a recorded axillary temperature of $37.5°C, (3) had clinical illness severe enough to warrant admission to hospital, and (4) were able to provide informed consent or had a surrogate available to do so. 13,14 Patients were excluded if they presented after trauma or were admitted to a nonmedical ward. During the study period, all admissions to the medical wards were screened for eligibility by study staff.…”

“…Sequencing libraries were multiplexed and analyzed using a 2 x 150 paired-end configuration on the Illumina HiSeq 4000 platform (Illumina, Inc., San Diego, CA). 13 As we did not assume a linear association between TB-LAM grade (analyzed as an ordinal independent variable) and log 10 -transformed immune mediator concentrations (analyzed as a continuous dependent variable), we created generalized additive models using the mgcv R-package. PLWH with pulmonary TB (sputum Xpert Ultra positive) and negative TB-LAM testing were included as a "grade zero" control group.…”