Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing

BMC Research Notes

Lan Anh Nguyen-Thi¹  William Hall²  Wayan T. Artama³  Kiew-Lian Wan⁴  Dela Ria Nesti⁵  Yutaka Suzuki⁶  Narumon Komalamisra⁷  Raweewan Srisawat⁷  Byoung-Kuk Na⁸  Gabriel O. Aboge⁹  Lucky R. Runtuwene^1,10  Ryuichiro Maeda^1,11  Junya Yamagishi^1,12  Yuki Eshita^1,12  Josef S. B. Tuda^1,13  Arthur E. Mongan^1,13  Wojciech Makalowski^1,14  Victoria Shabardina^1,15  Arnab Pain^1,16  Nuankanya Sathirapongsasuti^1,17 

[1] Center of Biomedical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam;Centre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland;Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia;Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia;Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia;Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan;Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand;Department of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju, South Korea;Department of Public Health, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya;Division 1, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan;Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan;Division of Biomedical Science, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary, Obihiro, Japan;Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan;Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia;Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany;Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain;Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia;Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan;Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand;

关键词: International collaboration;    Portable sequencing;    Field sequencing;    MinION;   

DOI  :  10.1186/s13104-022-05927-2

来源: Springer

【 摘 要 】

ObjectiveTo disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION’s operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.ResultsOne of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country.

【 授权许可】

CC BY