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Published on: December 28, 2017
Enhancing ascitic fungal infection diagnosis through next-generation sequencing: a pilot study in surgical ICU
Sara Posadas-Cantera1, Negin Mehrbarzin1, Simon Wetzel1,2
1Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany.
Objectives:
Ascites, often associated with critical pathologies such as liver cirrhosis or bowel perforation, can be complicated by fungal infection, increasing mortality especially in intensive care settings and demanding rapid diagnosis and adequate treatment. Traditional microbiological diagnostic methods have limited sensitivity in accurately identifying fungal pathogens in ascitic fluid. Alternative diagnostic methods may offer important insights to enable guiding of antifungal therapy and refining empirical treatment strategies. The objective of this study was to evaluate the potential of next-generation sequencing methods to identify specific fungal pathogens responsible for ascitic fluid infections.
Methods:
We prospectively collected 50 ascitic fluid samples from ICU patients with suspected ascites infection. In addition to standard culture-based microbiological testing, an ascitic fluid aliquot underwent fungal DNA isolation and was analyzed by next-generation sequencing (NGS) methods for identification of fungal species.
Results:
Of 50 ascitic samples collected, five samples showed growth of Candida spp. in culture. After DNA isolation and ITS2 PCR, detectable amplification was achieved in 10 samples. Sequencing of the 50 patients' samples identified facultative pathogenic fungi in 19 patients. In 15 cases, culture alone would not have permitted the identification of all facultative pathogenic fungi. The identification of fungal DNA by sequencing was significantly associated with poor patient outcome and a number of clinical parameters.
Conclusions:
Our results show a higher sensitivity for NGS-based diagnostic methods in the identification of ascitic fluid fungal infections compared to culture-based diagnostics. This may be beneficial especially for patients in a critical care setting, who have an increased prevalence of comorbidities and high mortality. The implementation of such methods in standard diagnosis will require increased standardization of the workflows and interpretation of the sequencing results with respect to patients' clinical picture.
Insights
Next-generation sequencing (NGS) offers higher sensitivity for diagnosing fungal infections in ascitic fluid compared to traditional methods. This advanced technique aids in identifying pathogens, improving patient outcomes in intensive care settings.
Area of Science:
- Medical Microbiology
- Genomics
- Critical Care Medicine
Background:
- Ascites, a critical condition linked to liver cirrhosis or bowel perforation, is prone to fungal infections.
- Fungal infections in ascites significantly increase mortality, particularly in intensive care units (ICUs).
- Current microbiological diagnostics for fungal pathogens in ascitic fluid lack sensitivity, necessitating improved methods.
Purpose of the Study:
- To evaluate the efficacy of next-generation sequencing (NGS) for identifying fungal pathogens in ascitic fluid.
- To compare the diagnostic performance of NGS with traditional culture-based methods.
Main Methods:
- Prospective collection of 50 ascitic fluid samples from ICU patients with suspected infection.
- Standard microbiological testing (culture) and fungal DNA isolation followed by NGS analysis.
- Analysis of the Internal Transcribed Spacer 2 (ITS2) region for fungal identification.
Main Results:
- NGS identified fungal pathogens in 19 out of 50 samples, significantly more than culture alone.
- Culture detected Candida spp. in only five samples.
- Fungal DNA detection by sequencing correlated with poorer patient outcomes and specific clinical parameters.
Conclusions:
- NGS demonstrates superior sensitivity for diagnosing fungal infections in ascitic fluid compared to standard cultures.
- This advanced diagnostic approach holds promise for guiding antifungal therapy and improving critical care patient outcomes.
- Standardization of NGS workflows and result interpretation is crucial for clinical implementation.
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