staramr

staramr predicts antimicrobial resistance genotypes and antibiograms from bacterial whole‑genome assemblies by scanning contigs against curated resistance databases and applying a gene–drug key.

Key Features:

• Database Integration: Uses ResFinder and PointFinder alongside a custom gene–drug key to identify known AMR genes and infer drug resistance.
• High‑Throughput Analysis: Processes genome assemblies at scale for large numbers of isolates.
• Phenotype Concordance: Demonstrated 99% concordance with broth microdilution antimicrobial susceptibility testing in 1,321 Salmonella enterica human isolates from Canada.
• Performance Metrics: Reported average sensitivity 91.2%, specificity 99.7%, positive predictive value 95.4%, and negative predictive value 99.1% for categorical resistance prediction.
• Detection of Genetic Mechanisms: Identifies acquired alleles and chromosomal mutations associated with AMR, detecting 64 unique acquired alleles and mutations in three chromosomal genes in the referenced study.
• Epidemiological Insight: Provides high‑resolution resistance mechanism data that can reveal emergence and distribution of resistance alleles.

Scientific Applications:

• Molecular Typing and Epidemiology: Links genomic resistance determinants with phenotypic profiles to support epidemiological analyses.
• Surveillance and Monitoring: Enables monitoring of AMR gene prevalence and spread across bacterial populations.
• Research and Development: Facilitates investigation of novel resistance mechanisms and genotype–phenotype relationships.

Methodology:

Scans genome contigs from whole‑genome sequencing assemblies against ResFinder and PointFinder to identify AMR genes and mutations, then applies a custom gene–drug key to predict the corresponding antibiogram and produce a summary report.