The combination of host gene expression profiles and metagenomic pathogen detection from plasma nucleic acid enables accurate sepsis diagnosis

The combination of host gene expression profiles and metagenomic pathogen detection from plasma nucleic acid enables accurate sepsis diagnosis

In a recent study published in Natural microbiology Researchers developed integrated host-microbe-plasma metagenomics to facilitate sepsis diagnosis.

Lernen: Integrierte Wirts-Mikroben-Plasma-Metagenomik zur Sepsis-Diagnose in einer prospektiven Kohorte kritisch kranker Erwachsener. Bildnachweis: Kateryna Kon/Shutterstock

background

Sepsis accounts for 20% of all deaths worldwide and 20 to 50% of all hospital deaths in the United States. Initial detection and identification of microbial infections is necessary for timely and effective antibiotic therapy, which is crucial for survival from sepsis. However, in more than 30% of cases, no etiological pathogens are detected. Distinguishing between sepsis and noninfectious systemic diseases is important because they often appear clinically similar during hospitalization.

About the study

In the present study, researchers developed a sepsis diagnostic tool that combines host transcriptional profiling with comprehensive pathogen identification.

In two tertiary care hospitals, the team conducted a prospective observational study of critically ill adult patients admitted from the emergency department (ED) to the intensive care unit (ICU). Patients were divided into five subgroups based on the presence or absence of sepsis. These patients included those who: (1) had clinically confirmed sepsis as well as confirmed bacterial bloodstream infection (SepsisBSI); (2) clinically confirmed sepsis and confirmed non-bloodstream infection (sepsis non-BSI); (3) suspected sepsis, characterized by negative clinical microbiological tests (suspected sepsis); (4) patients without evidence of sepsis and an explanation for their critical illness (no sepsis); or (5) patients with an indeterminate status (Indeterm).

By performing ribonucleic acid (RNA) sequencing on whole blood samples, the team first examined transcriptional variations between patients with clinically and microbiologically proven sepsis and those without symptoms of infection. A technique called Gene Set Enrichment Analysis (GSEA) detects clusters of genes within a data set with related biological functions.

A differential gene expression (DE) study in the SepsisBSI and Sepsisnon-BSI groups was conducted to identify further differences between sepsis patients with infections in the bloodstream and peripheral sites. The team developed a universal sepsis diagnostic classifier based on gene expression patterns in whole blood in response to the practical requirement to diagnose sepsis in both sepsisBSI and sepsis non-BSI patients. The team used a Bagged Support Vector Machine (bSVM) learning strategy to select the genes that most successfully distinguished patients with sepsis (SepsisBSI and Sepsisnon-BSI) from patients without sepsis (No-Sepsis).

After sequencing RNA from obtained patients whose plasma samples were available, a median of 2.3 × 107 readings was determined. In addition, DE analysis was performed to determine whether a biologically plausible signal could be used to distinguish patients with and without sepsis.

Results

Exacerbation of heart failure, overdose/poisoning, cardiac arrest, and pulmonary embolism were the most commonly diagnosed conditions in the no-sepsis group. Regardless of subgroup, most patients required vasopressor support and mechanical ventilation. Patients in SepsisBSI and Sepsisnon-BSI who had proven sepsis showed no difference from patients without sepsis in age, sex, race, ethnicity, APACHE III score, immunodeficiency, intubation status, peak white blood cell count, or 28-day mortality. In the group of patients without sepsis, all but one patient had two or more systemic inflammatory response syndrome (SIRS) criteria.

The study also found downregulation of signaling pathways associated with ribosomal RNA processing and translation, as well as upregulation of genes involved in innate immune signaling and neutrophil degranulation in sepsis patients. Using DE analysis, the team found 5,227 genes. The sepsis non-BSI cohort showed enrichment of genes associated with defensins, antimicrobial peptides, and G-alpha signaling, as well as other signaling pathways. On the other hand, the SepsisBSI cohort showed an enrichment of genes associated with, among other things, immunoregulatory interactions between non-lymphoid and lymphoid cells and CD28 signaling.

The bSVM model showed a mean cross-validation area under the receiver operating characteristic (ROC) curve (AUC) of 0.81. Samples with transcript counts below the quality control (QC) threshold had a lower mean input mass than samples with sufficient counts.

Interestingly, a number of differentially expressed genes have been identified as sepsis biomarkers, including elevated CD177, suppressed human leukocyte antigen-DR isotype (HLA-DRA), indicating a biologically significant transcriptome signature from plasma RNA. In the sepsis non-BSI group, metagenomic next-generation sequencing (mNGS) of plasma deoxyribonucleic acid (DNA) revealed three of eight pathogens of bacterial urinary tract infections (UTI) and two of 25 pathogens of bacterial lower respiratory tract infections (LRTI). None of the three patients with severe colitis caused by C. difficile had this pathogen. Additional potential bacterial pathogens not identified by culture were found in eight of 73 patients with confirmed sepsis.

Diploma

Overall, study results demonstrated that reliable sepsis diagnosis is facilitated by combining host gene expression profiling with identification of metagenomic pathogens from plasma nucleic acid. Future research is needed to verify and estimate the therapeutic benefit of this culture-independent diagnostic strategy.

Reference:

• Kalantar, K., Neyton, L., Abdelghany, M., Mick, E., Jauregui, A. & Caldera, S. et al. (2022). Integrierte Wirts-Mikroben-Plasma-Metagenomik zur Sepsis-Diagnose in einer prospektiven Kohorte kritisch kranker Erwachsener. Naturmikrobiologie. doi: 10.1038/s41564-022-01237-2 https://www.nature.com/articles/s41564-022-01237-2

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