Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study

PeerJ

article

Huan Chen¹  Jun Li²  Shanshan Yan³  Hui Sun⁴  Chuyi Tan⁴  Meidong Liu⁴  Ke Liu⁴  Huali Zhang⁴  Mingxiang Zou²  Xianzhong Xiao⁴ 

[1] Postdoctoral Research Station of Clinical Medicine & Department of Hematology, Third Xiangya Hospital, Central South University;Department of Clinical Laboratory, Xiangya Hospital, Central South University;Department of Intensive Medicine, Third Xiangya Hospital, Central South University;Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University

关键词: Shotgun metagenomic sequencing;    Culture;    Pathogen identification;    Infectious disease;    Antibiotic resistance;   

DOI  :  10.7717/peerj.11699

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.

【 授权许可】

CC BY