Specimen

Escherichia coli AR_0013 demo assembly

Escherichia coli · Escherichia_coli_AR_0013.fna

CIPROFLOXACIN — Likely to fail. Jump to detail.AMPICILLIN — Likely to fail. Jump to detail.GENTAMICIN — Likely to fail. Jump to detail.TETRACYCLINE — Likely to work. Jump to detail.CHLORAMPHENICOL — No call. Jump to detail.

Use
No call
Avoid

Genome annotation map

Genome 5,481,110 bpContigs 2Flagged regions 5

AMRFinderPlus · OKResFinder · OKBV-BRC · UNAVAILABLEXTree · UNAVAILABLE

ChromosomeCP032204.15,410,835 bp · 3 regions

05,410,835 bp

Plasmid 1CP032205.170,275 bp · 2 regions

070,275 bp

fluoroquinolone
aminoglycoside
beta-lactam
sulfonamide

Molecular structures

Interactive 3D backbones of the flagged resistance targets, sourced from the RCSB Protein Data Bank. Point-mutation sites are highlighted in red.

Loading 3D structure…

gyrA_S83L · Ciprofloxacin · RCSB PDB 1AB4 · resistance residue Ser83 highlighted

Cα backbone of the real experimental structure, rotating automatically. Red sphere marks the resistance-associated residue.

Assessment overview

Ciprofloxacin
91%
86%High
Known determinant
Ampicillin
88%
83%Moderate
Known determinant
Gentamicin
84%
78%Moderate
Known determinant
Chloramphenicol
52%
No call
Statistical association
Tetracycline
18%
79%Moderate
No known signal

Shaded band marks where a calibrated probability is treated as ambiguous and reported as a no-call.

Detailed information

Avoid — by confidence

CiprofloxacinLikely to fail

86%High confidenceKnown determinantgyrA_S83L

Calibrated confidence

Mechanism

AntibioticCiprofloxacin

TargetDNA gyrase / topoisomerase IV

OutcomeLikely to fail

gyrA_S83L: the determinant compromises the target, so the drug is likely ineffective.

Determinants

gyrA_S83L point mutation · AMRFinderPlus, ResFinder · WP_001301635.1
parC_S80I point mutation · AMRFinderPlus, ResFinder · WP_001393157.1

Statistical evidence

union:gyrA_s83l+2.34 · resistance-associated
agree:parC_s80i+1.12 · resistance-associated

Statistical association, not causation.

Molecular-target gate

PASS — Required quinolone target loci were detected and interpretable.

Model & calibration

baseline_amrfinder_logreg_v1-step2-calibrated · isotonic_regression (step2_isotonic_v1_split_v2) · distribution IN_DISTRIBUTION · nearest training distance 0.00072

AmpicillinLikely to fail

83%Moderate confidenceKnown determinantblaTEM-1B

Calibrated confidence

Mechanism

AntibioticAmpicillin

TargetPenicillin-binding proteins

OutcomeLikely to fail

blaTEM-1B: the determinant compromises the target, so the drug is likely ineffective.

Determinants

blaTEM-1B gene · AMRFinderPlus, ResFinder · WP_000027057.1

Statistical evidence

union:blaTEM-1B+1.91 · resistance-associated

Statistical association, not causation.

Molecular-target gate

PASS — Beta-lactam target compatibility checks passed.

Model & calibration

baseline_consensus_logreg_v1-step2-calibrated · isotonic_regression (step2_isotonic_v1_split_v2) · distribution IN_DISTRIBUTION · nearest training distance 0.00072

GentamicinLikely to fail

78%Moderate confidenceKnown determinantaac(3)-IId

Calibrated confidence

Mechanism

AntibioticGentamicin

Target30S ribosomal subunit

OutcomeLikely to fail

aac(3)-IId: the determinant compromises the target, so the drug is likely ineffective.

Determinants

aac(3)-IId gene · AMRFinderPlus, ResFinder · WP_000557454.1

Statistical evidence

agree:aac(3)-IId+2.08 · resistance-associated

Statistical association, not causation.

Molecular-target gate

PASS — Aminoglycoside target compatibility checks passed.

Model & calibration

baseline_consensus_logreg_v1-step2-calibrated · isotonic_regression (step2_isotonic_v1_split_v2) · distribution IN_DISTRIBUTION · nearest training distance 0.00072

Use — by confidence

TetracyclineLikely to work

79%Moderate confidenceNo known signal

Calibrated confidence

Mechanism

AntibioticTetracycline

Target30S ribosomal subunit

OutcomeLikely to work

no resistance determinant was found, so the target stays susceptible.

Statistical evidence

__mask__:AMRFinderPlus-0.36 · susceptibility-associated
__mask__:ResFinder-0.29 · susceptibility-associated

Statistical association, not causation.

Molecular-target gate

PASS — Molecular target compatibility gate passed and no required target was missing.

Model & calibration

baseline_resfinder_logreg_v1-step2-calibrated · isotonic_regression (step2_isotonic_v1_split_v2) · distribution IN_DISTRIBUTION · nearest training distance 0.00072

Needs laboratory confirmation

ChloramphenicolNo call

Calibrated probability resistant: 52% — inside the ambiguity band, reported as no-call rather than a direction.

Calibrated probability is inside the ambiguity band

Mechanism

AntibioticChloramphenicol

Target50S ribosomal subunit

OutcomeNo call

the signal is ambiguous, so no direction is asserted.

Target gate PASSEvidence AVAILABLEDistribution IN_DISTRIBUTION

Coverage

This report covers Escherichia coli and assesses 5 antibiotics: Ciprofloxacin, Ampicillin, Gentamicin, Tetracycline, Chloramphenicol.

Drugs outside this panel are not evaluated; absence from this report does not imply susceptibility.

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