ArticleJournal of microbiological methods2016
Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.
Article in Journal of microbiological methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
81 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Higher sensitivity and accuracy of synovial next-generation sequencing in comparison to culture in diagnosing periprosthetic joint infection: a systematic review and meta-analysis.Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA · 2023Pooled it
- Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis.Frontiers in neurology · 2022Pooled it
- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.Microbiology spectrum · 2026Article
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Metagenomic Next-generation Sequencing Compared With Blood Culture as First-line Diagnostic Method for Bloodstream Infection in Hematologic Patients With Febrile Neutropenia: A Multicenter, Prospective Study.Open forum infectious diseases · 2025Article
- Targeted sequencing ofmSystems · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?Expert review of molecular diagnostics · 2024Review
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Communications biology · 2024Article
- Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection.The Journal of molecular diagnostics : JMD · 2024Review
- Unified metagenomic method for rapid detection of microorganisms in clinical samples.Communications medicine · 2024Article
- Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions.International journal of medical microbiology : IJMM · 2024Article
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Research square · 2024Article
- Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses.Microbiome research reports · 2024Article
- Current Status and Perspectives of Diagnosis and Treatment of Periprosthetic Joint Infection.Infection and drug resistance · 2024Review
- Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections.Frontiers in cellular and infection microbiology · 2024Article
- Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis.Open forum infectious diseases · 2023Article
- High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion.Genomics, proteomics & bioinformatics · 2023Article
- Application of next-generation sequencing technology in the detection of pathogenic bacteria of the periprosthetic joint infection after arthroplasty.International wound journal · 2023Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.
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