MePIC, Metagenomic Pathogen Identification for Clinical Specimens

Japanese Journal of Infectious Diseases

Makoto Kuroda²  Fumihiko Takeuchi²  Akifumi Yamashita²  Tsuyoshi Sekizuka²  Yumiko Ogasawara²  Katsumi Mizuta¹ 

[1] Department of Microbiology, Yamagata Prefectural Institute of Public Health;Pathogen Genomics Center, National Institute of Infectious Diseases

关键词: next-generation sequencing;    metagenomics;    pathogen;   

DOI  :  10.7883/yoken.67.62

学科分类：传染病学

来源: National Institute of Infectious Diseases

【 摘 要 】

References(13)Cited-By(7)Next-generation DNA sequencing technologies have led to a new method of identifying the causative agents of infectious diseases. The analysis comprises three steps. First, DNA/RNA is extracted and extensively sequenced from a specimen that includes the pathogen, human tissue and commensal microorganisms. Second, the sequenced reads are matched with a database of known sequences, and the organisms from which the individual reads were derived are inferred. Last, the percentages of the organisms' genomic sequences in the specimen (i.e., the metagenome) are estimated, and the pathogen is identified. The first and last steps have become easy due to the development of benchtop sequencers and metagenomic software. To facilitate the middle step, which requires computational resources and skill, we developed a cloud-computing pipeline, MePIC: “Metagenomic Pathogen Identification for Clinical specimens.” In the pipeline, unnecessary bases are trimmed off the reads, and human reads are removed. For the remaining reads, similar sequences are searched in the database of known nucleotide sequences. The search is drastically sped up by using a cloud-computing system. The webpage interface can be used easily by clinicians and epidemiologists. We believe that the use of the MePIC pipeline will promote metagenomic pathogen identification and improve the understanding of infectious diseases.

【 授权许可】

Unknown