ArticleJournal of clinical microbiology2017
Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.
Article in Journal of clinical microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
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
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Metagenomic next-generation sequencing (mNGS) versus tissue culture technique (TCT) in diagnosis of spinal infection: a systematic review and meta-analysis.Scientific reports · 2025Pooled it
- Comparing saliva collection and DNA extraction methods for saliva-based microbiome profiling.Frontiers in microbiology · 2026Article
- Whole genome sequencing of Cryptosporidium from low DNA inputs without whole genome amplification.Molecular biology reports · 2025Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.Microbial genomics · 2025Article
- Article
- The tumor microbiome in cancer progression: mechanisms and therapeutic potential.Molecular cancer · 2025Review
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.BMC medical genomics · 2024Article
- Benchmarking DNA isolation methods for marine metagenomics.Scientific reports · 2023Article
- Pathogen detection in suspected spinal infection: metagenomic next-generation sequencing versus culture.European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society · 2023Review
- Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis.Open forum infectious diseases · 2023Article
- Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites.Nature communications · 2023Article
- Case report: A toxoplasmic encephalitis in an immunocompromised child detected through metagenomic next-generation sequencing.Frontiers in public health · 2023Article
- Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections withFrontiers in cellular and infection microbiology · 2023Article
- Characterization of cerebrospinal fluid (CSF) microbiota at the time of initial surgical intervention for children with hydrocephalus.PloS one · 2023Article
- Cost-saving population genomic investigation ofEcology and evolution · 2022Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units.Microbiology spectrum · 2022Article
- Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. Variations in the number of background reads, the genera identified in the background, and the number of reads from known pathogens known to be present in the samples were observed between kits. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. This approach also resulted in the presence of contaminant bacterial DNA and yielded fewer reads from the known pathogens. These findings highlight the impact that WGA kit selection can have on metagenomic analysis of low-biomass samples and the importance of the careful selection and consideration of the implications of using these tools.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.