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Updated: Jun 11, 2025

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Damage-associated molecular patterns in bacteraemic infection, including a comparative analysis with bacterial DNA, a
Helena Alpkvist1,2, Ingrid Ziegler3, Paula Mölling4
1Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
Abstract:
Damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs) are key triggers of inflammation in sepsis. However, they have rarely been studied simultaneously. Thus, in the present study of patients with bacteraemic infection, we aimed to study how DAMP dynamics are linked to disease severity and outcome and to compare diagnostic and prognostic properties of a DAMP and a previously analysed PAMP (16S rDNA). In a prospective study of adult patients hospitalized with culture-proven community-onset bacteraemic infection, caused by Streptococcus pneumonia (n = 30), Staphylococcus aureus (n = 27), or Escherichia coli (n = 26), dynamics of a PAMP, i.e. 16S rDNA, have previously been presented. For the present study, blood samples obtained on hospital days 1-2 (when blood culture was positive), 3-4, 7 ± 1, 14 ± 2, and 28 ± 4 were analysed for four different DAMPs, i.e., nuclear DNA (nDNA), mitochondrial DNA (mtDNA), heat shock protein 90 alpha (HSP90α), and extracellular high mobility group box 1 (HMGB1). Sepsis was defined according to the Sepsis-3 criteria. The study outcomes were sepsis at admission and negative outcome, defined as intensive care unit (ICU) admission and/or death within 60 days. Of 83 study patients, sepsis was noted in 41 patients (49%) and a negative outcome was noted in 17 patients (20%). nDNA had areas under the receiver operating characteristic (ROC) curves of 0.78 for sepsis and 0.76 for negative outcome, which were higher than those of the other DAMPs and additional biomarkers (CRP, IL-6, IL-8, and IL-10). The nDNA and positive 16S rDNA results on day 1-2 were correlated with each other (r = 0.68, p < 0.001). Multivariate analyses showed that high day 1-2 concentrations of both nDNA and 16S rDNA were independently associated with sepsis. In addition, high day 1-2 concentration of nDNA was independently associated with negative outcomes. While 16S rDNA dissipated from the circulation within days, nDNA concentrations remained elevated throughout the follow-up period in patients with negative outcome. In conclusion, nDNA outperformed the other DAMPs regarding sepsis detection and outcome prediction. Both nDNA (a DAMP) and 16S rDNA (a PAMP) were independently linked to sepsis; nDNA was also associated with negative outcomes and persisted elevated in such cases. This highlights nDNA as an interesting marker within sepsis pathogenesis and as a promising clinical biomarker, warranting further studies.
Insights
Nuclear DNA (nDNA) shows promise as a sepsis biomarker, outperforming other damage-associated molecular patterns (DAMPs) in detecting sepsis and predicting negative outcomes. Elevated nDNA levels indicate sepsis severity and persist in patients with poor outcomes.
Area of Science:
- Sepsis pathogenesis and biomarker discovery
- Infectious disease immunology
- Clinical diagnostics
Background:
- Sepsis is triggered by damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs), but simultaneous study is rare.
- Understanding DAMP dynamics in bacteraemic infection is crucial for assessing disease severity and patient outcomes.
Purpose of the Study:
- To investigate the dynamics of four DAMPs (nDNA, mtDNA, HSP90α, HMGB1) in patients with bacteraemic infection.
- To compare the diagnostic and prognostic capabilities of DAMPs against a PAMP (16S rDNA) and other biomarkers.
- To correlate DAMP levels with sepsis severity and patient outcomes.
Main Methods:
- Prospective study of 83 adult patients with community-onset bacteraemic infection (Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli).
- Analysis of blood samples for nDNA, mtDNA, HSP90α, and HMGB1 on multiple hospital days.
- Comparison of DAMP performance against 16S rDNA, CRP, IL-6, IL-8, and IL-10 for sepsis and negative outcome prediction.
Main Results:
- Nuclear DNA (nDNA) demonstrated superior diagnostic accuracy (ROC curves 0.78 for sepsis, 0.76 for negative outcome) compared to other DAMPs and biomarkers.
- High day 1-2 concentrations of both nDNA and 16S rDNA were independently associated with sepsis.
- Elevated nDNA levels on day 1-2 were independently linked to negative outcomes and persisted in patients with poor prognosis.
Conclusions:
- Nuclear DNA (nDNA) is a promising biomarker for sepsis detection and outcome prediction, outperforming other DAMPs.
- Both nDNA (DAMP) and 16S rDNA (PAMP) are independently associated with sepsis, with nDNA also predicting negative outcomes.
- Persistent elevation of nDNA in patients with negative outcomes highlights its role in sepsis pathogenesis and clinical utility.
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