Albertsen, Mads

Nielsen, Hans Linde

Nielsen, Morten Eneberg

Søgaard, Kirstine Kobberøe

English

The gold standard of clinical microbiology diagnostics is to culture the pathogen, which takes 1-3 days and has poor sensitivity. Due to the long turnaround time, critically ill patients are administered empiric broad-spectrum antibiotics prior to pathogen identification and an estimated ~20% of patients receive ineffective treatment causing excess mortality. The wide deployment of broad-spectrum antibiotics is also the main reason for the development of multi resistant bacteria, a health crisis predicted by WHO to cause 20% of all deaths in 2050 if there is no change in our use of antibiotics.To overcome the limitations of current methods, we are exploring the use of DNA sequencing on the MinION platform for pathogen identification in critically ill hospitalised patients. This has the potential to revolutionise clinical microbiology diagnostics by lowering turnaround times from multiple days to &lt;6 hours, providing medical doctors with the basis for a more informed choice of treatment. We will utilise methods developed for archaeogenetics (the study of ancient DNA) to enrich microbial DNA with the aim of obtaining higher sensitivity at a reduced cost. Furthermore, we will use methods from machine learning to separate DNA profiles of diseased from that of healthy individuals to increase analysis specificity

    Aalborg UniversitetFrom days to hoursDevelopment and implementation of metagenomic DNA- sequencing in clinical microbiologydiagnosticsNielsen, Morten Eneberg; Søgaard, Kirstine Kobberøe; Nielsen, Hans Linde; Albertsen, MadsPublication date:2021Link to publication from Aalborg UniversityCitation for published version (APA):Nielsen, M. E., Søgaard, K. K., Nielsen, H. L., & Albertsen, M. (2021). From days to hours: Development andimplementation of metagenomic DNA- sequencing in clinical microbiology diagnostics. Abstract from DanishMicrobiological Society congress 2021, Copenhagen, Denmark.General rightsCopyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright ownersand it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.            - Users may download and print one copy of any publication from the public portal for the purpose of private study or research.            - You may not further distribute the material or use it for any profit-making activity or commercial gain            - You may freely distribute the URL identifying the publication in the public portal -Take down policyIf you believe that this document breaches copyright please contact us at vbn@aub.aau.dk providing details, and we will remove access tothe work immediately and investigate your claim.Downloaded from vbn.aau.dk on: November 19, 2022From days to hours: Development and implementation of metagenomic DNA-sequencing in clinical microbiology diagnostics Morten Eneberg Nielsen1, Kirstine Kobberøe Søgaard2, Hans Linde Nielsen2, Mads Albertsen1 1Aalborg University, Center for Microbial Communities, Dept. of Chemistry and Bioscience, Aalborg, Denmark 2Aalborg University Hospital, Dept. of Clinical Microbiology, Aalborg, Denmark The gold standard of clinical microbiology diagnostics is to culture the pathogen, which takes 1-3 days and has poor sensitivity. Due to the long turnaround time, critically ill patients are administered empiric broad-spectrum antibiotics prior to pathogen identification and an estimated ~20% of patients receive ineffective treatment causing excess mortality. The wide deployment of broad-spectrum antibiotics is also the main reason for the development of multi resistant bacteria, a health crisis predicted by WHO to cause 20% of all deaths in 2050 if there is no change in our use of antibiotics.  To overcome the limitations of current methods, we are exploring the use of DNA sequencing on the MinION platform for pathogen identification in critically ill hospitalised patients. This has the potential to revolutionise clinical microbiology diagnostics by lowering turnaround times from multiple days to <6 hours, providing medical doctors with the basis for a more informed choice of treatment. We will utilise methods developed for archaeogenetics (the study of ancient DNA) to enrich microbial DNA with the aim of obtaining higher sensitivity at a reduced cost. Furthermore, we will use methods from machine learning to separate DNA profiles of diseased from that of healthy individuals to increase analysis specificity.  

From days to hours:Development and implementation of metagenomic DNA- sequencing in clinical microbiology diagnostics

https://vbn.aau.dk/files/470646292/2021_09_14_DMS_Abstract_MEN.pdf

From days to hours:Development and implementation of metagenomic DNA- sequencing in clinical microbiology diagnostics

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