data/rag/knowledge_base/Cupriavidus/gilardii.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Cupriavidus",
  "species": "gilardii",

  "overview": {
    "short": "Cupriavidus gilardii is a Gram-negative, aerobic, non-fermentative rod increasingly recognised as an opportunistic human pathogen.",
    "clinical_context": "Associated with bloodstream, respiratory, and device-related infections, particularly in immunocompromised patients."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Positive",
    "Capsule": "Negative",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar",
      "Chocolate Agar"
    ],
    "Colony Morphology": [
      "Smooth",
      "Grey",
      "Non-pigmented"
    ],
    "Oxygen Requirement": "Aerobe",
    "Growth Temperature": "20//37",
    "Catalase": "Positive",
    "Oxidase": "Positive",
    "Indole": "Negative",
    "Urease": "Variable",
    "Citrate": "Negative",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Variable",
    "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": "Citrate",
      "value": "Negative",
      "importance": "medium",
      "notes": "Helps separate C. gilardii from other citrate-positive Cupriavidus species."
    },
    {
      "field": "Nitrate Reduction",
      "value": "Negative",
      "importance": "medium",
      "notes": "Differentiates from denitrifying environmental relatives."
    }
  ],

  "common_confusions": [
    {
      "genus": "Burkholderia",
      "reason": "Shared oxidase positivity and non-fermentative metabolism."
    },
    {
      "genus": "Ralstonia",
      "reason": "Phylogenetic similarity and overlapping biochemical profile."
    }
  ],

  "when_to_question_identification": [
    "Oxidase negativity argues against C. gilardii.",
    "Any glucose fermentation suggests misidentification.",
    "Anaerobic growth is inconsistent."
  ],

  "recommended_next_tests": [
    {
      "test": "Arginine dihydrolase",
      "reason": "Supports placement among Cupriavidus species.",
      "api_kit": "API 20 NE"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable discrimination from Burkholderia and Ralstonia.",
      "api_kit": "Not applicable"
    }
  ]
}