Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study
Huan Chen,
Jun Li,
Shanshan Yan,
Hui Sun,
Chuyi Tan,
Meidong Liu,
Ke Liu,
Huali Zhang,
Mingxiang Zou,
Xianzhong Xiao
Affiliations
Huan Chen
Postdoctoral Research Station of Clinical Medicine & Department of Hematology, Third Xiangya Hospital, Central South University, Changsha, China
Jun Li
Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
Shanshan Yan
Department of Intensive Medicine, Third Xiangya Hospital, Central South University, Changsha, China
Hui Sun
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
Chuyi Tan
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
Meidong Liu
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
Ke Liu
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
Huali Zhang
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
Mingxiang Zou
Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
Xianzhong Xiao
Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
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.
