Less than 6 hours of incubation of the blood culture is enough for the identification of pathogens using nanopore sequencing

Bloodstream infections (BSIs) and sepsis are major health problems and are responsible for millions of deaths each year across the globe. The traditional blood cultures, used for identifying sepsis-causing pathogens and their antibiotic susceptibility or resistance, usually take 2-4 days. It is crucial to prescribe appropriate antibiotics to septic patients as early as possible to reduce mortality risk and antibiotic resistance. In this study, the most common sepsis-causing bacteria are tested for their detection limit in blood cultures by inoculating them into BD BACTEC blood culture bottles with healthy human blood and then incubating them in a laboratory incubator. The bacterial inoculum used for spiking was less than 50 CFU/ml. The samples incubated for 3,6,9 and 12h were sequenced using nanopore sequencing. We have shown that we successfully identified the pathogen and AMR-encoding genes by incubating the blood cultures in a standard laboratory incubator for 5 h and then using nanopore sequencing, In one blood culture sample (E. coli CCUG17620) having 40 CFU/ml, we were still able to identify the pathogen. Identifying different AMR genes took around 40 m to 3 h (mecA gene – took the longest time) of nanopore sequencing. This method can be advantageous in future clinical aspects for diagnosing BSIs. It can significantly reduce the time to detect pathogens and provide early information to clinicians for prescribing appropriate antibiotics.