ArticleJournal of clinical microbiology2022
The Clinical Utility of Two High-Throughput 16S rRNA Gene Sequencing Workflows for Taxonomic Assignment of Unidentifiable Bacterial Pathogens in Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.
Article in Journal of clinical microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis 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
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 23 citations in OpenAlex.
- Traumatic CSF rhinorrhea associated with COVID-19 testing: a case series and systematic review.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2025Pooled it
- NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.BMC bioinformatics · 2026Article
- Gene Expression Profiling of SARS-CoV-2 Host Entry Factors in Nasal and Oral Cavities: Evidence from Hospitalized COVID-19 Patients.Current microbiology · 2026Article
- Validation of a long-read 16S rRNA-gene sequencing approach for analysis of clinical samples and bacterial identification in a routine clinical laboratory.Frontiers in microbiology · 2026Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.Journal of clinical microbiology · 2025Article
- Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Effects of the sampling time on the vaginal microbiota in healthy pregnant women: a prospective observational study.AJOG global reports · 2025Article
- Article
- Community-acquired pneumonia caused by Micrococcus antarcticus: a rare case report.BMC infectious diseases · 2024Article
- Article
- EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale.Microbiology spectrum · 2024Article
- Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.Molecular diagnosis & therapy · 2023Review
- Application of MALDI-TOF MS for enumerating bacterial constituents of defined consortia.Applied microbiology and biotechnology · 2023Article
- Alteration of gut microbiota in wild-borne long-tailed macaques after 1-year being housed in hygienic captivity.Scientific reports · 2023Article
- The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids.Frontiers in microbiology · 2023Article
- Detection of Microorganisms in Body Fluid Samples.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing.Frontiers in microbiology · 2023Article
- Empyema caused byFrontiers in public health · 2022Article
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial pathogens that cannot be identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming, and low throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests that are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by the respective built-in programs (MiSeq Reporter software of Illumina and Epi2me of Nanopore) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of Nanopore 16S was 96.36%, which was identical to that of Sanger 16S and better than that of Illumina 16S (69.07%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78 h and 8.25 h, respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.
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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.