Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream

281 positive blood cultures were analyzed using long-read sequencing to identify pathogens and antimicrobial resistance genes. The dataset includes supplementary figures and data on DNA extraction kit performance, AMR gene detection counts, and time-to-detection metrics for specific pathogens. It was authored by Nicole Lerminiaux and last updated on 2026-05-21.

Use Cases

• Benchmarking AMR gene detection tools based on the reported counts of 992 genes in assemblies and 849 in reads.
• Evaluating DNA extraction kit performance for sequencing based on A260/A230 and A260/A280 purity ratios.
• Analyzing time-to-detection for S. aureus toxin genes across 30 positive blood cultures.
• Comparing host read depletion methods (adaptive vs. normal sampling) based on the number of host reads and bases removed.

Strengths

• Includes data from 281 positive blood cultures, providing a substantial sample size for analysis.
• Compares two AMR gene detection methods (assembly-based and read-based) with specific counts of correctly identified genes.
• Provides performance metrics for DNA extraction kits, with clear purity ratio measurements.
• Data is shared under a permissive CC-BY-4.0 license.

Limitations

• Row count and column-level documentation are unknown, which may limit suitability assessment.
• The description focuses on supplementary figures; the structure and variables of the underlying CSV/XLSX files must be inferred after download.
• Data may reflect the specific experimental and methodological bias inherent to the study on figshare.

Provenance

Source

figshare

Collection Method

Long-read sequencing of positive blood cultures, with analysis using tools like StarAMR and KmerResistance.

Freshness

Last updated 2026-05-21 09:45:56; freshness should be verified.