Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands.
Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan.
PLoS Negl Trop Dis. 2020 Dec 16;14(12):e0008897. doi: 10.1371/journal.pntd.0008897. eCollection 2020 Dec.
Eumycetoma is a neglected tropical disease most commonly caused by the fungus Madurella mycetomatis. Identification of eumycetoma causative agents can only be reliably performed by molecular identification, most commonly by species-specific PCR. The current M. mycetomatis specific PCR primers were recently discovered to cross-react with Madurella pseudomycetomatis. Here, we used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification.
Predicted-protein coding sequences unique to M. mycetomatis were first identified in BLASTCLUST based on E-value, size and presence of orthologues. Primers were then developed for 16 unique sequences and evaluated against 60 M. mycetomatis isolates and other eumycetoma causing agents including the Madurella sibling species. Out of the 16, only one was found to be specific to M. mycetomatis.
We have discovered a predicted-protein coding sequence unique to M. mycetomatis and have developed a new species-specific PCR to be used as a novel diagnostic marker for M. mycetomatis.
足放线菌肿是一种被忽视的热带病，最常见的病原体是真菌棘白菌素属。只有通过分子鉴定，最常见的是基于种特异性的 PCR，才能可靠地鉴定出足放线菌肿的病原体。最近发现，目前用于棘白菌素属的特异性 PCR 引物与假棘白菌素属真菌存在交叉反应。在这里，我们使用比较基因组学的方法来开发一种新的用于物种鉴定的棘白菌素属特异性 PCR。
首先，根据 E 值、大小和同源物的存在，在 BLASTCLUST 中基于预测蛋白编码序列识别棘白菌素属特有的序列。然后，针对 16 个独特序列开发引物，并对 60 株棘白菌素属分离株和其他足放线菌肿病原体（包括棘白菌素属的姐妹种）进行评估。在这 16 个序列中，只有一个被发现是棘白菌素属特有的。
我们发现了一个棘白菌素属特有的预测蛋白编码序列，并开发了一种新的种特异性 PCR，可作为棘白菌素属的新型诊断标记物。
