data/rag/knowledge_base/Cedecea/genus.json

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

  "overview": {
    "short": "Cedecea species are rare, Gram-negative, facultatively anaerobic rods within the Enterobacterales, infrequently isolated from clinical specimens.",
    "clinical_context": "Occasionally associated with opportunistic infections such as bacteremia, wound infections, and respiratory infections, particularly 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"
  },

  "field_notes": {
    "Lactose Fermentation": "Typically non-lactose fermenting on MacConkey Agar.",
    "Motility": "Motile by peritrichous flagella, helping distinguish from Klebsiella.",
    "ONPG": "Positive despite lactose non-fermentation, indicating beta-galactosidase activity."
  },

  "key_differentiators": [
    {
      "field": "ONPG",
      "expected": "Positive",
      "distinguishes_from": ["Salmonella", "Shigella"],
      "notes": "ONPG positivity helps separate Cedecea from non-ONPG Enterobacterales."
    },
    {
      "field": "Ornithine Decarboxylase",
      "expected": "Positive",
      "distinguishes_from": ["Enterobacter"],
      "notes": "Ornithine positivity is useful in narrowing uncommon Enterobacterales."
    },
    {
      "field": "Lactose Fermentation",
      "expected": "Negative",
      "distinguishes_from": ["Enterobacter", "Klebsiella"],
      "notes": "Non-lactose fermentation supports Cedecea over common lactose fermenters."
    }
  ],

  "common_confusions": [
    {
      "genus": "Enterobacter",
      "reason": "Shared citrate positivity and VP positivity can overlap biochemically."
    },
    {
      "genus": "Serratia",
      "reason": "ONPG positivity and motility may overlap in atypical isolates."
    }
  ],

  "when_to_question_identification": [
    "Strong lactose fermentation on MacConkey Agar.",
    "Indole positivity (not typical for Cedecea).",
    "H2S production present."
  ],

  "recommended_next_tests": [
    {
      "test": "ONPG test",
      "reason": "Supports identification among rare Enterobacterales.",
      "api_kit": "API 20E"
    },
    {
      "test": "Ornithine decarboxylase",
      "reason": "Helpful discriminator for Cedecea species.",
      "api_kit": "API 20E"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Recommended due to rarity and biochemical overlap with other Enterobacterales."
    }
  ],

  "supported_species": [
    "davisae",
    "lapagei"
  ]
}