Reproducible bioinformatics portfolio
AMR Insight
Genotype-aware exploration of recorded ciprofloxacin resistance in Escherichia coli from public isolate records.
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Rates describe this selected database snapshot only; they are not population prevalence.
Explore the included records
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| BioSample | Assembly | Country | Year | Specimen | Phenotype | AMR genotypes |
|---|
Explore a genotype profile
This displays association with recorded phenotype labels. It is not a patient risk score and does not recommend an antibiotic.
Model-estimated probability of a resistant label
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Research exploration only—not a clinical threshold.
Held-out performance
Coefficients use the transformed feature scale. Their sign shows model association, not causation or isolated biological importance.
Study design and boundaries
Research question. Can isolate metadata and selected AMRFinderPlus genotype indicators distinguish recorded ciprofloxacin-resistant from susceptible E. coli isolates?
Inclusion. Exact E. coli records with a unique BioSample accession, valid collection year, and one unambiguous ciprofloxacin phenotype (R or S). Intermediate, conflicting, and missing phenotypes are excluded.
Model. Class-weighted logistic regression with broad source metadata, collection year, AMR genotype count, quinolone-resistance markers, selected QRDR substitutions, and beta-lactamase-family indicators. The newest viable years are held out.
Limits. Submitter-supplied AST methods and breakpoints may differ across laboratories and time. Submission patterns strongly shape the dataset. Genotype calls may correlate with study origin, laboratory practice, lineage, geography, and time. Strong discrimination is not causal or clinical validity.
Intended use. Portfolio research, reproducible bioinformatics, and hypothesis generation—not diagnosis, treatment selection, or population surveillance.