Nanopore sequencing technology identifies the first case of Penicilliosis marneffei in Shaanxi Province
MA Lin1, LIU Dong-li1, MAO Ling-feng2, WANG Yi-qun3, DING Long4, WANG An-li1
1. Shaanxi Provincial Center for Disease Control and Prevention,Xi'an 710054,China; 2. Hangzhou Baocheng Biotechnology Co. Ltd. , Hangzhou 310000, China; 3. Wangfeng Health Center, Hancheng City, Shaanxi Province, Hancheng 715400, China; 4. First Department of Infection, Xi'an Eighth Hospital, Xi'an 710000, China
Abstract：This study aimed to detect the etiology of one case of severe infectious disease; to identify the source of infection, and to provide a basis for clinical diagnosis and treatment. To investigate the epidemiological history, clinical symptoms and signs of the patient, and to perform general laboratory tests, we extracted the patient's blood nucleic acids, and searched for pathogen information through metagenomic analysis technology based on nanopore sequencing. The general primers for fungal ITS, Penicillium marneffei PCR, Leishmania protozoa and histocapsular cytoplasm were used for identification. The patient's blood sample results were confirmed with fungal biphasic culture. The patient had a history of unprotected homosexual and heterosexual intercourse, and often traveled to Southeast Asia. The clinical symptoms and signs were consistent with those of HIV infection. The preliminary HIV screening and confirmation test were positive, and testing with antibody against Leishmaniasis was negative. The actual sequencing time required by the MinION nanopore sequencer was 3.5 hours. A total of 84 000 reads were obtained, with a mean sequence length of 7 088.7 bases: the longest was 87 471 bases, and the shortest was 562 bases. The total amount of data was 495 Mb. The base calling data were uploaded to EPI2Me and analyzed with the WIMP Workflow. There were 63 617 pieces of human genome data and 13 pieces of Penicillium marneffei sequences. The sequencing results of fungal ITS amplification identified Penicillium marneffei, and the PCR results were positive for Penicillium marneffei and negative for histoplasma capsulatum. Fungal biphase culture at 25 ℃ revealed mycelial and yeast colonies at 37 ℃, which were identified as Penicillium marneffei. The patient was infected with Penicillium marneffei with HIV. This is the first reported case in Shaanxi Province, China. Metagenomic analysis based on nanopore sequencing can be used as an indicator for rapid diagnosis of difficult infectious diseases in clinical practice.
马琳, 刘东立, 毛凌峰, 王益群, 丁龙, 王安礼. 纳米孔测序技术鉴定陕西省首例马尔尼菲青霉菌感染病例[J]. 中国人兽共患病学报, 2021, 37(9): 851-857.
MA Lin, LIU Dong-li, MAO Ling-feng, WANG Yi-qun, DING Long, WANG An-li. Nanopore sequencing technology identifies the first case of Penicilliosis marneffei in Shaanxi Province. Chinese Journal of Zoonoses, 2021, 37(9): 851-857.
2021, Vol. 37 
