Clinical Metagenomic Sequencing Reports from Hospitalized Patients, 2024-2025

1,981 specimen-specific first orders for clinical metagenomic next-generation sequencing from a single-center retrospective study between January 1, 2024, and December 31, 2025. Report-interpreted positivity varied by specimen type, with bronchoalveolar lavage fluid highest at 90.0% and cerebrospinal fluid lowest at 26.2%. The dataset, authored by Jian-min Ren and shared on figshare, characterizes specimen-specific reporting patterns for pathogens like Epstein-Barr virus and Candida albicans.

Use Cases

• Compare report positivity rates based on specimen type (BALF, blood, CSF, tissue) described in the study
• Analyze the frequency of reported organisms like Epstein-Barr virus and Klebsiella pneumoniae across different specimen categories
• Investigate patterns of mixed pathogen detection among positive orders, which was reported for 76.7% of BALF orders
• Study the subset of orders that underwent PMseq-RNA testing for RNA virus analysis

Strengths

• Includes 1,981 specimen-specific first orders with clear counts per type (973 BALF, 473 blood, 240 CSF, 122 tissue)
• Provides precise report positivity percentages with 95% confidence intervals for each primary specimen group
• Contains a defined subset of 277 orders (14.0%) that underwent PMseq-RNA testing for RNA virus analysis

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 bias inherent to the source

Provenance

Source

figshare

Collection Method

Single-center retrospective observational study using routine clinical mNGS data

Time Range

January 1, 2024 to December 31, 2025

Freshness

Last updated 2026-05-20 10:44:12; freshness should be verified