MePIC, Metagenomic Pathogen Identification for Clinical Specimens

Abstract

SUMMARY: 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.Next-generation DNA sequencing technologies have led to a new method of identifying the causative agent of infectious diseases in hospitalized patients and during outbreaks (1,2). By directly sequencing millions of DNA/RNA molecules in a specimen and matching the sequences to those in a database, pathogens can be inferred. The analysis comprises three steps. First, the nucleotide sequences of the specimen, which includes the pathogen, human tissue and commensal microorganisms, are read using a next-generation sequencer. Second, from bioinformatic processing of the reads, the organisms from which the individual reads were derived are inferred. Last, the percentages of the organisms' genomic sequences in the specimen are estimated, and the pathogen is identified. Although the first and last steps have become easy due to the development of benchtop sequencers and metagenomic software, the middle step still requires computational resources and bioinformatic skill. To facilitate the middle step, we developed a cloud-computing pipeline that is easy and fast.

A Case of an Aortic Abscess around the Elephant Trunk

“…10) It is expected that bacterial identification will be performed using metagenome analysis in the future. 11) For the treatment of prosthetic vascular graft infection in the thoracic aortic area, Coselli et al 1) reported a composite of aortic graft reconstruction and omental filling procedures after re-thoracotomy and debridement in 1999, resulting in a high 1-year mortality rate of approximately 30%. In 1984, Hargrove et al 12) reported successful infection control by omental filling without removal of infected prosthetic grafts.…”

A food‐borne outbreak of gastroenteritis due to genotype G1P[8] rotavirus among adolescents in Japan

“…However, some outbreaks of RV infection in adults have been reported (5). This report describes an outbreak of gastroenteritis due to genotype G1P [8] RV in adolescents in Tochigi prefecture, Japan.…”

“…The obtained raw short reads ($1 million reads per sample) were analyzed by the MePIC server (8) to characterize potential pathogens. Sequence analysis of VP4 and VP7 genes by NGS suggested that this sample contained G1P [8] rotavirus. Therefore, VP4 and VP7 genes of RV were amplified and detected from all of the samples using nested RT-PCR (9, 10).…”

“…Molecular epidemiologic analyses showed that the causative agent was genotype G1P [8] rotavirus (RV), this being detected in stool samples from both the patients and the asymptomatic food handlers. The detected RV strains were closely related genetically.…”

“…Among rotavirus A, G, and P genotypes are defined by genes encoding outer capsid proteins VP7 and VP4, respectively (2). Previous reports have suggested that RV group A genotypes G1P [8], G2P [4], G3P [8], G4P [8] and G9P [8] are dominant in various countries (3,4). Epidemiological studies have suggested that most RV infections occur in infants (1).…”