ReviewFrontiers in public health2018
Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics.
Review in Frontiers in public health, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
17 citing papers in PubMed.
- Vaginal microbiome and preterm birth: Composition, mechanisms and microbiota‑directed therapies (Review).International journal of molecular medicine · 2025Review
- Typing ofMicroorganisms · 2025Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes.Access microbiology · 2024Article
- Article
- Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection.Journal of advanced research · 2022Article
- Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of ClinicalMicroorganisms · 2022Article
- Host DNA depletion can increase the sensitivity ofFrontiers in microbiology · 2022Article
- A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients.mSystems · 2021Article
- Microbiome-immune interactions in tuberculosis.PLoS pathogens · 2021Review
- Clinical Pathogen Genomics.Clinics in laboratory medicine · 2020Review
- The pregnancy microbiome and preterm birth.Seminars in immunopathology · 2020Review
- Optimization of sample preparation for culture-independent sequencing ofMicrobial genomics · 2020Article
- Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples.Journal of clinical microbiology · 2020Article
- Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study.Frontiers in microbiology · 2020Article
- Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges.Foodborne pathogens and disease · 2019Review
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.
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