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amr-surveillance

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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

When to use

• screening clinical or surveillance isolates for AMR
• distinguishing acquired vs intrinsic vs point-mutation resistance
• calling rpoB / katG / pncA / gyrA / mgrB mutations
• reconciling AMRFinderPlus vs RGI vs ResFinder disagreement
• contextualising carbapenemases or mcr alleles on plasmids
• predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue
• building a hAMRonized multi-lab AMR surveillance pipeline

When not to use

• Mtb screening without TB-Profiler or Mykrobe
• running AMRFinderPlus without --organism for point-mutation detection

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