data/rag/knowledge_base/Achromobacter/denitrificans.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Achromobacter",
  "species": "denitrificans",

  "overview": {
    "short": "Achromobacter denitrificans is a Gram-negative, aerobic, non-fermenting rod characterized by strong nitrate reduction and denitrification capability.",
    "clinical_context": "Rarely associated with human infection and more commonly encountered in environmental samples."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Positive",
    "Capsule": "Unknown",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Smooth",
      "Grey"
    ],
    "Oxygen Requirement": "Aerobic",
    "Growth Temperature": "20//37",
    "Catalase": "Positive",
    "Oxidase": "Positive",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Variable",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Positive",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Positive",
    "Glucose Fermentation": "Negative",
    "Lactose Fermentation": "Negative",
    "Sucrose Fermentation": "Negative",
    "Maltose Fermentation": "Negative",
    "Mannitol Fermentation": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Negative",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "K/K",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Polar"
  },

  "species_markers": [
    {
      "field": "Nitrate Reduction",
      "value": "Positive",
      "importance": "high",
      "notes": "Denitrification capability is characteristic of A. denitrificans."
    }
  ],

  "common_confusions": [
    {
      "species": "Achromobacter xylosoxidans",
      "reason": "Shared oxidase positivity and non-fermentative metabolism."
    }
  ],

  "when_to_question_identification": [
    "Absence of nitrate reduction argues against A. denitrificans.",
    "Clinical isolation should prompt confirmation due to rarity."
  ],

  "recommended_next_tests": [
    {
      "test": "Nitrate reduction and denitrification testing",
      "reason": "Defining feature of this species."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Required for reliable species-level identification."
    }
  ]
}