Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Sci Rep. 2020 May 6;10(1):7622. doi: 10.1038/s41598-020-64616-x.


Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blood Culture / methods*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • Drug Resistance, Microbial / genetics*
  • Escherichia coli / genetics
  • Gene Transfer, Horizontal
  • Nanopore Sequencing / methods*
  • Plasmids / genetics*
  • Salmonella / genetics
  • Time Factors


  • DNA, Bacterial