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Abstract：
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
摘要：
下一代测序（NGS）技术最近已经超出了研究领域，并开始成熟到临床应用。这里,我们回顾了NGS在真菌感染实验室诊断中的应用.自2014年第一例病例报告以来，描述了NGS诊断的>300例真菌感染病例。据报道，肺孢子虫是主要的真菌，构成约25%的真菌检测。在~12.5%的病例中，NGS检测到一种以上的真菌。对于NGS诊断的Jirovecii感染，所有91例患者均患有肺炎,只有1例HIV阳性.这与吉罗韦西氏疟原虫感染的一般流行病学非常不同，其中HIV感染是最重要的危险因素。NGS诊断的马尔尼菲塔拉菌感染的流行病学也不同于其一般流行病学，只有3/11的患者是HIV阳性。使用NGS进行实验室诊断的主要优点是它可以检测到所有病原体，特别是当最初的微生物调查是没有结果的。当NGS的成本进一步降低时，专业知识更广泛可用，克服了其他障碍，NGS将是真菌感染实验室诊断的有用工具，特别是对于难以生长的真菌和低真菌负荷的病例。
