ArticlePeerJ2021
Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 15 citations in OpenAlex.
- The Potential of Bioinformatics in Revolutionizing Disease Diagnosis in Sub-Saharan Africa: A Narrative Review.Health science reports · 2026Article
- Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort Against Infectious Diseases.Antibiotics (Basel, Switzerland) · 2026Article
- Food-borne bacterial pathogens: emerging approaches in detection and prevention.Archives of microbiology · 2026Review
- Article
- Multidrug resistance, diagnostic challenges, and treatment gaps inBiomolecules & biomedicine · 2025Review
- Leveraging innovative diagnostics as a tool to contain superbugs.Antonie van Leeuwenhoek · 2025Review
- Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.Frontiers in plant science · 2025Article
- Review
- Review
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- Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis.International journal of molecular sciences · 2022Review
- Pentraxin-3 Is a Strong Biomarker of Sepsis Severity Identification and Predictor of 90-Day Mortality in Intensive Care Units via Sepsis 3.0 Definitions.Diagnostics (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEarly 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.
methodsTo 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.
resultsShotgun 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.
conclusionsPathogen 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.
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