Needle David B, Reboul Guillaume, Mitchell Patrick K, Rothenheber Derek, Marra Nicholas J, Cronk Brittany D, Patel Neeti G, Goodman Laura B
New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH 03824, USA.
Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Microorganisms. 2025 Feb 27;13(3):533. doi: 10.3390/microorganisms13030533.
The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were , sp., sp. (likely ), sp., sp., atypical , spp., , , , , , , and . We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.
在福尔马林固定石蜡包埋（FFPE）组织中鉴定真菌病原体是人类和兽医学中尚未满足的需求，因此需要采用不依赖序列的方法来鉴定新出现的病原体。本文利用11份基于配对新鲜组织样本的标准检测确诊为真菌病的FFPE活检标本，评估宏条形码技术。这些病例包括来自3只狗、3只猫、1只箱龟、1只山羊、1只普通潜鸟和1只灰树蛙的组织。这些病例中新鲜组织的诊断结果分别为： 种、 种、 种（可能为 ）、 种、 种、非典型 、 种、 、 、 、 、 、 。我们将内转录间隔区1（ITS1）和28S D1核糖体RNA（rRNA）基因遗传标记与多种生物信息学策略相结合，以鉴定FFPE组织样本中的真菌病原体，成功率为9/11。这些方法可以让仅接收FFPE组织并发现真菌病原体的诊断人员对病原体进行分类，并且在FFPE组织是唯一存档组织的回顾性研究中可能具有价值。此外，这些技术对于研究DNA保存欠佳的微生物群落的研究人员可能有用。
