Dual RNA-seq of clinical adult sepsis samples (TOPS study) to characterize host-pathogen interactions

Blood samples (0.5 ml) of 8 adults with blood culture-confirmed bacterial sepsis and 3 healthy adults were collected. A previously optimized host-bacterial RNA extraction protocol was used to isolate leukocyte and bacterial RNA. Purified RNA was depleted or rRNA and underwent deep sequencing using a 150 bp paired-end sequencing run on a NovaSeq 6000 (Illumina). Host and bacterial sequencing reads were aligned in silico and bioinformatic analyses were used to explore host and bacterial transcriptional responses during sepsis.