Kidd Sarah E, Chen Sharon C-A, Meyer Wieland, Halliday Catriona L
National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia.
Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia.
Front Microbiol. 2020 Jan 14;10:2903. doi: 10.3389/fmicb.2019.02903. eCollection 2019.
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
侵袭性真菌病（IFD）在免疫功能低下和其他重症人群中给全球带来的负担日益加重，包括由固有耐药或对抗真菌药物敏感性较低的病原体引起的疾病。早期诊断包括准确检测和鉴定病原体以及抗真菌药物耐药性，对于实现最佳患者预后至关重要。许多基于分子的诊断方法具有良好的临床实用性，不过结果的解释应结合临床背景。在IFD为鉴别诊断之一时，泛真菌PCR检测可直接从临床标本中快速检测/鉴定真菌种类，特异性良好；当在标本（包括石蜡包埋组织）中见到菌丝时，敏感性也很高。血液成分的PCR检测在高危血液学患者筛查中具有良好效用，当获得两个阳性PCR结果时，阴性预测值（NPV）和阳性预测值（PPV）分别为94%和70%。PCR检测的标准化和商业化现已使各实验室之间能够直接比较结果，商业化检测还可同时检测常见的唑类耐药突变。PCR检测的标准化程度不高，唯一获得美国食品药品监督管理局（FDA）批准的商业系统（T2念珠菌检测系统）仅能检测五种最常见的念珠菌；虽然T2念珠菌检测系统在念珠菌血症患者中优于血培养，但其在常规诊断中的作用尚不明确。毛霉目特异性PCR检测在血液成分中检测特定属的应用越来越多。在许多诊断实验室中，定量实时PCR已取代显微镜检查和免疫荧光染色，不过在未感染HIV的患者中区分感染情况可能存在问题。对于分离株的种类鉴定，双基因座（ITS和α）的DNA条形码技术提供最佳准确性，而下一代测序（NGS）技术则可对遗传多样性进行高度鉴别分析，包括用于暴发调查和耐药性特征分析。分子技术的进步将进一步提升常规真菌诊断水平。
