A new method using rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study

Background Bloodstream infections (BSIs) remain a major cause of mortality, in part due to many patients developing sepsis or septic shock. To survive sepsis, it is paramount that effective antimicrobial therapy is initiated rapidly to avoid excess mortality, but the current gold-standard to identify the pathogen in BSIs, blood culturing, has great limitations with a long turnaround time and a poor sensitivity. This delay to correct empiric broad-spectrum antimicrobial treatments leads to excess mortality and antimicrobial resistance development. Methods In this study we developed a metagenomic next-generation sequencing (mNGS) assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. The method was evaluated in a prospective observational clinical study (n=40) in an emergency ward setting, where a study sample was taken from the same venipuncture as a blood culture sample from patients with a suspected BSI. Findings Nanopore mNGS confirmed all findings in patients with a positive blood culture (n=11), and identified pathogens relevant to the acute infection in an additional 11 patients with a negative blood culture. In an analysis of potential impact on the antibiotic treatment, we found that 59% (n=13) of mNGS positive answers could have impacted the treatment, with five cases of a change from ineffective to effective therapy. Interpretation This study demonstrates that culture-independent Nanopore mNGS directly on blood plasma could be a feasible alternative to blood culturing for infection diagnostics for patients admitted with a severe infection or sepsis. The method identified a relevant pathogen in patients with a broad range of etiologies including urinary tract infections and lower respiratory tract infections. With a turnaround time of 6 hours the method could provide unprecedented speed and sensitivity in BSI diagnostics. ### Competing Interest Statement MEN, SMK, HLN, and MA are in the process of filing patents related to algorithms presented in this study. MEN has stocks in Oxford Nanopore Technologies plc. ### Funding Statement The study was funded by a research grant from the Independent Research Fund Denmark (Grant no. 2096-00079B). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol was reviewed and accepted by The Scientific Ethics Committee for the North Denmark Region (N-20220015). The study was also approved according to GDPR (article 30) regulation for the North Denmark Region (Project-ID: F2023-056). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Individual patient metadata is shared in the appendix. Microbial DNA sequencing data from positive mNGS tests is deposited in NCBI SRA and is accessible with the BioProject identifier PRJNA1108520. On reasonable request study protocol and informed consent form, will be shared from the publication date and onwards by contacting the corresponding author (ma@bio.aau.dk).