Supplementary data files from a study estimating optimal sample sizes for genomic surveillance of E. coli and Klebsiella bloodstream infections in England. The data includes sample accessions, assembly metrics, isolate-level annotations, and AMR gene annotations derived from a 6-month genomic survey (NEKSUS). The dataset was authored by Dorottya Nagy and last updated in May 2026.
Use Cases
- Estimating required sample sizes for genomic surveillance based on MLST and plasmid diversity.
- Analyzing regional specificity of plasmid populations and Klebsiella MLSTs mentioned in the study.
- Modeling the frequency distribution of AMR genes and fastBAPS clusters to inform sampling strategies.
- Assessing the representativeness of national sampling frames for bacterial bloodstream infections.
Strengths
- Includes data from a 6-month genomic survey of English bloodstream infections.
- Provides specific sample size estimates for achieving 80% coverage of MLSTs, plasmids, fastBAPS clusters, and AMR genes with 95% certainty.
- Data is stratified by region, allowing for analysis of geographic variation.
Limitations
- Column-level documentation is absent; field semantics must be inferred after download.
- Row count is unknown, which may limit suitability assessment.
- The dataset's temporal coverage is limited to the 6-month NEKSUS study period.
Provenance
- Source
- figshare, authored by Dorottya Nagy.
- Collection Method
- Derived from a regionally-stratified genomic survey of English bloodstream infections (NEKSUS), with analysis using Bayesian bootstrapping.
- Time Range
- Covers a 6-month period, specific dates not provided.
- Freshness
- Last updated 2026-05-19 17:10:22; freshness should be verified.
- Geography
- England, with regional stratification.