Clinical Metagenomic Sequencing Reports from a Single-Center Study, 2024-2025

A single-center retrospective observational study analyzed 1,981 clinical metagenomic next-generation sequencing (mNGS) orders from hospitalized patients between January 1, 2024, and December 31, 2025. The data, authored by Jian-min Ren and shared on figshare, compares report-interpreted positivity and pathogen detection across bronchoalveolar lavage fluid, blood, cerebrospinal fluid, and tissue specimens. It includes specimen-specific positivity rates and lists frequently reported organisms such as Epstein-Barr virus and Candida albicans.

Use Cases

• Compare specimen-specific positivity rates for clinical mNGS based on the reported 90.0% positivity for BALF versus 26.2% for CSF.
• Analyze patterns of mixed pathogen detection based on the description of at least 2 distinct pathogens reported in 76.7% of positive BALF orders.
• Rank frequently detected organisms across specimen types based on the reported frequencies of Epstein-Barr virus (n=485) and Candida albicans (n=285).
• Assess the prevalence of RNA virus testing based on the subset of 277 orders (14.0%) that underwent PMseq-RNA testing.

Strengths

• Dataset includes 1,981 specimen-specific first mNGS orders with detailed counts per specimen type (e.g., 973 BALF, 473 blood).
• Provides precise, specimen-level positivity rates with 95% confidence intervals (e.g., 90.0% for BALF, 26.2% for CSF).
• Reports frequencies for specific pathogens, such as Epstein-Barr virus (n=485) and Candida albicans (n=285).
• Distinguishes between DNA-only and RNA-tested orders, with 277 orders (14.0%) having PMseq-RNA testing.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data is from a single-center study, which may reflect institutional biases in testing and reporting practices.

Provenance

Source

figshare

Collection Method

Retrospective observational study using routine clinical mNGS data from a single center.

Time Range

January 1, 2024 to December 31, 2025

Freshness

Last updated 2026-05-20 10:44:13; freshness should be verified.