RNA Sequencing of Sepsis Patients Informs Tests to Quickly Diagnose Pathogens and Resistance

Diagnosis of infection in patients with sepsis takes days via culture, and appropriate treatment of pathogens is delayed awaiting results. We hypothesize that we can use RNA sequencing from patients with sepsis to identify novel targets for faster nucleic acid-based tests.

Cohort study of sepsis patients admitted to the intensive care unit with RNA sequencing was done after obtaining the consent. RNA sequencing data that did not map to the human genome were then aligned to resistance genes and pathogen genomes and used to design novel polymerase chain reaction (PCR) tests. These tests were correlated with blood culture diagnosis and clinical outcomes.

Forty-six patients were enrolled, and samples from 87 time points were collected. These samples resulted in 8.6 billion RNA sequencing reads to identify pathogen RNA. PCR target discovery focused on positive blood cultures (n = 40 total) due to Escherichia coli (five samples), Staphylococcus aureus (six samples), and Pseudomonas aeruginosa (three samples) as well as identification of resistance genes. From RNA sequencing reads, 40 targets were defined and tested by quantitative PCR. In a cohort of patients (9 of 46) with available samples, some of the proposed PCRs identified all cases of positive blood cultures ( P. aeruginosa and S. aureus ); E. coli had no positive blood cultures in this cohort.

RNA sequencing from patients with sepsis can identify RNA from pathogens causing the infection. This is used to design PCR primers that identify patients with positive blood cultures. Translation of these primers to clinical microbiology machines will allow the diagnosis faster than blood culture.