Drug Antibiogram Tally

Deduplicate isolate/drug results and compute drug-specific susceptibility percentages with a caller minimum sample size; breakpoints must already be applied.

Description

An antibiogram aggregates already interpreted isolate/drug results.

An antibiogram aggregates already interpreted isolate/drug results. Repeated records should not inflate a drug's denominator, and each drug can have a different number of tested isolates.^[1]

Deduplicate isolate/drug results and compute drug-specific susceptibility percentages with a caller minimum sample size; breakpoints must already be applied.

When to use Drug Antibiogram Tally

Use this tool to deduplicate isolate/drug results and compute drug-specific susceptibility percentages with a caller minimum sample size; breakpoints must already be applied.

Prepare the sample, count, growth or assay measurements requested by this tool. Confirm units, sampling periods and reporting bases; supply independently established comparison criteria where requested.

How to use Drug Antibiogram Tally and understand its results

Prepare the sample, count, growth or assay measurements requested by this tool. Confirm units, sampling periods and reporting bases; supply independently established comparison criteria where requested.
Enter isolateIds, drugNames, resultCodes, minimumIsolates using the field table and calculation rules, then run the tool.
Read drugs, testedIsolateCounts, susceptiblePercentages, adequateSampleFlags. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
isolateIds	Isolate ids	list of string	Required
drugNames	Drug names	list of string	Required
resultCodes	Result codes	list of string	Required
minimumIsolates	Minimum isolates	integer; minimum: 1	Required

Enter aligned nonempty isolate IDs, drug names and exact S/I/R codes, plus positive integer minimumIsolates. Identical repeated isolate/drug calls are deduplicated; conflicting repeats are errors. Drug groups follow first appearance. Return drug names, distinct tested counts, S-only percentages and binary 0/1 adequate-sample flags using inclusive minimum counts.

Paired lists must be nonempty and have equal lengths.

susceptiblePercent_drug=100 × distinct isolates called S/distinct tested isolates

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
drugs	Drugs	list of string
testedIsolateCounts	Tested isolate counts	list of number
susceptiblePercentages	Susceptible percentages	list of number
adequateSampleFlags	Adequate sample flags	list of number

json

{
  "input": {
    "isolateIds": [
      "A",
      "B",
      "A"
    ],
    "drugNames": [
      "amp",
      "amp",
      "mero"
    ],
    "resultCodes": [
      "S",
      "R",
      "S"
    ],
    "minimumIsolates": 2
  },
  "output": {
    "drugs": [
      "amp",
      "mero"
    ],
    "testedIsolateCounts": [
      2,
      1
    ],
    "susceptiblePercentages": [
      50,
      100
    ],
    "adequateSampleFlags": [
      1,
      0
    ]
  }
}

Limitations and assumptions

Breakpoints must already have been applied. I is not counted as S by this tally, and no broader patient/time deduplication or clinical guidance is inferred. Labels are compared exactly without trimming their stored spelling.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Supplied Disk Zone Interpretation: Apply caller-supplied disk-diffusion zone breakpoints; I retains the supplied classification scheme and is not universally interpreted as intermediate. For a complementary task, use Disk QC Range Audit: Audit observed QC disk zones against supplied strain-, drug-, and method-specific inclusive ranges.

References

Drug Antibiogram Tally — tool.io

Similar or alternative tools

Supplied Disk Zone Interpretation
Apply caller-supplied disk-diffusion zone breakpoints; I retains the supplied classification scheme and is not universally interpreted as intermediate.
Disk QC Range Audit
Audit observed QC disk zones against supplied strain-, drug-, and method-specific inclusive ranges.