Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany.
Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Solna, Sweden.
Front Cell Infect Microbiol. 2024 Nov 1;14:1441805. doi: 10.3389/fcimb.2024.1441805. eCollection 2024.
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.
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.
Of 50 ascitic samples collected, five samples showed growth of 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.
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.
腹水常与肝硬化或肠穿孔等危急病症相关，可能并发真菌感染，增加死亡率，尤其是在重症监护环境中，并需要快速诊断和适当的治疗。传统的微生物诊断方法在准确识别腹水真菌病原体方面的灵敏度有限。替代诊断方法可能提供重要的见解，以指导抗真菌治疗并完善经验性治疗策略。本研究的目的是评估下一代测序方法在鉴定导致腹水感染的特定真菌病原体方面的潜力。
我们前瞻性地收集了 50 例来自 ICU 疑似腹水感染患者的腹水样本。除了标准的基于培养的微生物学检测外，还对腹水样本进行了真菌 DNA 分离，并通过下一代测序 (NGS) 方法分析，以鉴定真菌物种。
在收集的 50 个腹水样本中，有 5 个样本在培养中显示出 spp. 的生长。经过 DNA 分离和 ITS2 PCR 后，在 10 个样本中实现了可检测的扩增。对 50 名患者样本的测序鉴定出 19 名患者存在兼性致病真菌。在 15 例中，仅培养无法鉴定出所有兼性致病真菌。通过测序鉴定真菌 DNA 与患者不良预后和多项临床参数显著相关。
与基于培养的诊断方法相比，基于 NGS 的诊断方法在鉴定腹水真菌感染方面具有更高的灵敏度。这可能对处于重症监护环境中的患者特别有益，因为他们的合并症患病率更高，死亡率更高。在标准诊断中实施此类方法需要增加工作流程的标准化，并根据患者的临床情况对测序结果进行解释。
