data/rag/knowledge_base/Cedecea/davisae.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Cedecea",
  "species": "davisae",

  "overview": {
    "short": "Cedecea davisae is a rare, Gram-negative, facultatively anaerobic rod within the Enterobacterales.",
    "clinical_context": "Occasionally isolated from opportunistic infections including bacteremia and respiratory infections, primarily in immunocompromised patients."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Positive",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "MacConkey Agar",
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Smooth",
      "Grey",
      "Moist"
    ],
    "Oxygen Requirement": "Facultative Anaerobe",
    "Growth Temperature": "30//37",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Positive",
    "Methyl Red": "Negative",
    "VP": "Positive",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Positive",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Positive",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Positive",
    "Ornitihine Decarboxylase": "Positive",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Negative",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Positive",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Positive",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Positive",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Positive",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Variable",
    "TSI Pattern": "A/A",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Peritrichous"
  },

  "species_markers": [
    {
      "field": "Ornithine Decarboxylase",
      "value": "Positive",
      "importance": "high",
      "notes": "Key discriminator separating C. davisae from C. lapagei."
    },
    {
      "field": "Lysine Decarboxylase",
      "value": "Negative",
      "importance": "medium",
      "notes": "Supports differentiation from some Enterobacter species."
    }
  ],

  "common_confusions": [
    {
      "species": "Cedecea lapagei",
      "reason": "Closely related species with overlapping biochemical reactions."
    },
    {
      "genus": "Enterobacter",
      "reason": "Shared citrate and VP positivity may cause misidentification."
    }
  ],

  "when_to_question_identification": [
    "Ornithine decarboxylase is negative.",
    "Lactose fermentation is present.",
    "Indole is positive."
  ],

  "recommended_next_tests": [
    {
      "test": "Ornithine decarboxylase",
      "reason": "Primary discriminator between Cedecea species.",
      "api_kit": "API 20E"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable confirmation for rare Enterobacterales species."
    }
  ]
}