ArticleHeliyon2021
Targeted metagenomics using next generation sequencing in laboratory diagnosis of culture negative endophthalmitis.
Article in Heliyon, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed, 27 citations in OpenAlex.
- Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.Microorganisms · 2026Review
- Areas of uncertainty in endophthalmitis care.World journal of clinical cases · 2026Review
- Detection of Pathogens by a Novel User-Developed Broad-Range BR 16S PCR rRNA Polymerase Chain Reaction/Gene Sequencing Assay: Multiyear Experience in a Large Canadian Healthcare Zone.Microorganisms · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- The microbial strategies for the management of chemical pesticides: A comprehensive review.Current research in microbial sciences · 2026Review
- Role of Sanger Sequencing in the Early Diagnosis of Infective Endophthalmitis: Experience From a Pilot Study.Cureus · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- International consensuses and guidelines on diagnosing and managing fungal endophthalmitis by the Asia-Pacific Vitreo-retina Society (APVRS), the Academy of the Asia-Pacific Professors of Ophthalmology (AAPPO), and the Asia-Pacific Society of Ocular Inflammation and Infection (APSOII).Eye and vision (London, England) · 2025Review
- Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis.BMC infectious diseases · 2025Article
- QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.Microbiology spectrum · 2025Article
- Leveraging innovative diagnostics as a tool to contain superbugs.Antonie van Leeuwenhoek · 2025Review
- The role of mNGS in the diagnosis of talaromycosis and case series.BMC infectious diseases · 2025Article
- Detection of methicillin resistance of Staphylococcus aureus in vitreous humor using MALDI-TOF MS and Fc-MBL@FeScientific reports · 2024Article
- Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections.Pathogens (Basel, Switzerland) · 2024Article
- 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
- Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis.BMJ open ophthalmology · 2023Article
- The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis.International ophthalmology · 2023Article
- Update on Current Microbiological Techniques for Pathogen Identification in Infectious Endophthalmitis.International journal of molecular sciences · 2022Review
- Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review.International journal of ophthalmology · 2022Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To study the feasibility of 16S rRNA metagenomics using next generation sequencing (NGS) along with broad range PCR assay for 762 bp region of 16S rRNA gene with Sanger's sequencing, in microbial diagnosis of culture negative endophthalmitis. Vitreous fluid from 16 culture negative and one culture positive endophthalmitis patients, admitted to a tertiary care hospital were processed for targeted metagenomics. NGS of 7 variable regions of 16S rRNA gene was done using Ion Torrent Personal Genome Machine (PGM). Sequence data were analyzed using Ion Reporter software using QIIME and BLSATN tools and Greengenes and NCBI-Genbank databases. Bacterial genome sequences were detected in 15 culture negative and culture positive vitreous specimens. The sequence reads varied between 25,245-540,916 with read length between 142bp-228bp and coverage depth was 41.0X and 81.2X. Operational taxonomic unit (OTUs) of multiple bacterial genera and species were detected in 13 culture negative vitreous specimens and OTUs of a single bacterial species were detected in 2 culture negative and 1 culture positive specimens; one negative specimen had no bacterial DNA. Maximum numbers of OTUs detected by NGS for a bacterial species from any vitreous specimen was the one which was detected and identified by Sanger's sequencing in broad range PCR. All the bacteria were belonging to clinically relevant species. Broad range PCR with sequencing failed to identify bacteria from 5 of the 16 (31.25%) culture negative vitreous specimens. Metagenomics could detect and identify bacterial pathogens in 15 of the 16 culture negative vitreous specimen's up to species level. With rapidly decreasing cost, metagenomics has a potential to be used widely in endophthalmitis diagnosis, in which culture negativity is usually high.
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Registered trials
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.