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
Sepsis is a life-threatening syndrome triggered by infection and accompanied by high mortality, with antimicrobial resistances (AMRs) further escalating clinical challenges. The rapid and reliable detection of causative pathogens and AMRs are key factors for fast and appropriate treatment, in order...
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| Main Authors: | , , , , , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
17 May 2024
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| In: |
International journal of molecular sciences
Year: 2024, Volume: 25, Issue: 10, Pages: 1-16 |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms25105463 |
| Online Access: | Verlag, kostenfrei, Volltext: https://doi.org/10.3390/ijms25105463 Verlag, kostenfrei, Volltext: https://www.mdpi.com/1422-0067/25/10/5463 
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| Author Notes: | Mirko Sonntag, Vanessa K. Elgeti, Yevhen Vainshtein, Lucca Jenner, Jan Mueller, Thorsten Brenner, Sebastian O. Decker and Kai Sohn |
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| 245 | 1 | 0 | |a 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 |c Mirko Sonntag, Vanessa K. Elgeti, Yevhen Vainshtein, Lucca Jenner, Jan Mueller, Thorsten Brenner, Sebastian O. Decker and Kai Sohn |
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| 520 | |a Sepsis is a life-threatening syndrome triggered by infection and accompanied by high mortality, with antimicrobial resistances (AMRs) further escalating clinical challenges. The rapid and reliable detection of causative pathogens and AMRs are key factors for fast and appropriate treatment, in order to improve outcomes 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 targeted eight pathogens across three kingdoms and ten AMRs in a proof-of-concept study. SUPSETS was successfully tested in an experimental research study on the first ten clinical samples and revealed comparable results to clinical metagenomics while clearly outperforming blood culture. Several clinically relevant AMRs could be additionally detected. Furthermore, SUPSETS provided first pathogen and AMR-specific sequencing reads within minutes of starting sequencing, thereby potentially decreasing time-to-results to 11-13 h and suggesting diagnostic potential in sepsis. | ||
| 650 | 4 | |a Anti-Bacterial Agents | |
| 650 | 4 | |a antimicrobial resistances | |
| 650 | 4 | |a Bacteria | |
| 650 | 4 | |a Blood Culture | |
| 650 | 4 | |a cell-free DNA | |
| 650 | 4 | |a Cell-Free Nucleic Acids | |
| 650 | 4 | |a DNA, Bacterial | |
| 650 | 4 | |a Drug Resistance, Bacterial | |
| 650 | 4 | |a Humans | |
| 650 | 4 | |a Multiplex Polymerase Chain Reaction | |
| 650 | 4 | |a Nanopore sequencing | |
| 650 | 4 | |a Nanopore Sequencing | |
| 650 | 4 | |a next-generation sequencing | |
| 650 | 4 | |a Polymerase Chain Reaction | |
| 650 | 4 | |a precision diagnostics | |
| 650 | 4 | |a real-time diagnostics | |
| 650 | 4 | |a sepsis | |
| 650 | 4 | |a Sepsis | |
| 650 | 4 | |a suppression PCR | |
| 700 | 1 | |a Elgeti, Vanessa K. |e VerfasserIn |4 aut | |
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| 700 | 1 | |a Mueller, Jan |e VerfasserIn |4 aut | |
| 700 | 1 | |a Brenner, Thorsten |d 1978- |e VerfasserIn |0 (DE-588)130125709 |0 (DE-627)491713363 |0 (DE-576)189360607 |4 aut | |
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| 700 | 1 | |a Sohn, Kai |e VerfasserIn |0 (DE-588)1119923964 |0 (DE-627)873031229 |0 (DE-576)177398981 |4 aut | |
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