Nanopore-targeted sequencing for simultaneous diagnosis of suspected sepsis and early targeted therapy

Bloodstream infection can rapidly progress to sepsis with each delay to appropriate therapy.In particular, patients with advanced age, active cancer, hematological disease, immunocompromised status, or critical illness are prone to severe infection (1).The main characteristics of infection in these patients are extremely rapid progression and resistance to conventional broad-spectrum antibiotics.Early identification of pathogens is imperative for reducing the risk of death (2).However, standard diagnostic methods rely on culturing, which has poor sensitivity and is not suitable for atypical infections with fastidious organisms.Even with typical pathogenic microorganisms, the turnaround time ranges from 48 to 96 hours.Therefore, culturing is always too slow to guide targeted antimicrobial therapy.Based on third-generation sequencing technology, we directly incorporated a panel of microbial tags and developed nanopore-targeted sequencing (NTS).Using real-time NTS, we successfully identified pathogens under complex host-microorganism settings, such as whole blood samples.This approach can reduce testing time and clinical turnaround time to less than 2 and 6 hours, respectively, enabling early targeted therapy.The detailed protocol and evaluation of NTS have been published elsewhere as a methodological study (3,4).Briefly, instead of a metagenomic analysis, a panel of 27,668 microbial tags (including bacteria, fungi, viruses, drugresistant genes, and atypical pathogens), were incorporated