Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Suppression PCR-Based Selective Enrichment Sequencing for Pathogen and Antimicrobial Resistance Detection on Cell-Free DNA in Sepsis - A Targeted, Blood Culture Independent Approach for Rapid Pathogen and Resistance Diagnostics in Septic Patients

Mirko Sonntag
ORCID logo ,
Vanessa K. Elgeti
,
Yevhen Vainshtein
ORCID logo ,
Lucca Jenner
,
Jan Mueller
ORCID logo ,
Thorsten Brenner
,
Sebastian O. Decker
ORCID logo ,
Kai Sohn
*
Version 1 : Received: 19 April 2024 / Approved: 22 April 2024 / Online: 22 April 2024 (10:13:14 CEST)

How to cite: Sonntag, M.; Elgeti, V.K.; Vainshtein, Y.; Jenner, L.; Mueller, J.; Brenner, T.; Decker, S.O.; Sohn, K. Suppression PCR-Based Selective Enrichment Sequencing for Pathogen and Antimicrobial Resistance Detection on Cell-Free DNA in Sepsis - A Targeted, Blood Culture Independent Approach for Rapid Pathogen and Resistance Diagnostics in Septic Patients. Preprints 2024, 2024041390. https://doi.org/10.20944/preprints202404.1390.v1 Sonntag, M.; Elgeti, V.K.; Vainshtein, Y.; Jenner, L.; Mueller, J.; Brenner, T.; Decker, S.O.; Sohn, K. Suppression PCR-Based Selective Enrichment Sequencing for Pathogen and Antimicrobial Resistance Detection on Cell-Free DNA in Sepsis - A Targeted, Blood Culture Independent Approach for Rapid Pathogen and Resistance Diagnostics in Septic Patients. Preprints 2024, 2024041390. https://doi.org/10.20944/preprints202404.1390.v1

Abstract

Sepsis is a life-threatening syndrome triggered by infection and accompanied by high mortality, with antimicrobial resistances (AMRs) further escalating clinical challenges. Rapid and reliable detection of causative pathogens and AMRs are key factors for fast and appropriate treatment, in order to improve outcome in septic patients. However, current sepsis diagnostics based on blood culture is limited by low sensitivity and specificity while current molecular approaches fail to enter clinical routine. Therefore, we developed a Suppression PCR-based selective enrichment sequencing approach (SUPSETS), providing a molecular method combining multiplex suppression PCR with Nanopore sequencing to identify most common sepsis-causative pathogens and AMRs using plasma cell-free DNA. Applying only 1 mL of plasma, we target eight pathogens across three kingdoms and ten AMRs in a proof-of-concept study. SUPSETS was successfully tested on first ten clinical samples and revealed comparable results to clinical metagenomics while clearly outperforming blood culture. Several clinically relevant AMRs could be detected additionally. Furthermore, SUPSETS provided first pathogen and AMR-specific sequencing reads within minutes of starting sequencing, thereby potentially decreasing time to results to 11 - 13 hours and suggesting diagnostic potential in sepsis.

Keywords

sepsis; antimicrobial resistances; cell-free DNA; precision diagnostics; Next-Generation sequencing; suppression PCR; real-time diagnostics; nanopore sequencing

Subject

Medicine and Pharmacology, Epidemiology and Infectious Diseases

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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