Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing

Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2 – 4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTECTM bottles in standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on eight blood samples spiked with clinical isolates from the five most prevalent sepsis-causing species. The results showed that pathogen identification was possible at as low as 102 – 104 CFU/mL, achieved after just two hours of incubation and within 40 minutes of nanopore sequencing. Moreover, all the antimicrobial resistance genes (ARGs) were identified at 103 – 107 CFU/mL, achieved after incubation for five hours and only 10 minutes to 3 hours of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between seven to nine hours. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.