data/rag/knowledge_base/Enterobacter/genus.json

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

  "overview": {
    "short": "Enterobacter species are Gram-negative, facultatively anaerobic rods within the Enterobacterales, commonly isolated from clinical and environmental sources.",
    "clinical_context": "Often recovered from opportunistic infections including urinary tract, respiratory, and bloodstream infections."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Variable",
    "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": "10//45",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Variable",
    "Urease": "Variable",
    "Citrate": "Positive",
    "Methyl Red": "Negative",
    "VP": "Positive",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Positive",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Variable",
    "Nitrate Reduction": "Positive",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Positive",
    "Ornithine Decarboxylase": "Variable",
    "Ornitihine Decarboxylase": "Variable",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Positive",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Positive",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Positive",
    "Rhamnose Fermentation": "Variable",
    "Arabinose Fermentation": "Positive",
    "Raffinose Fermentation": "Variable",
    "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": "Often delayed or variable on MacConkey Agar.",
    "Motility": "Most species are motile, but non-motile strains occur.",
    "Indole": "Indole reactions vary by species and are not genus-defining."
  },

  "key_differentiators": [
    {
      "field": "VP",
      "expected": "Positive",
      "distinguishes_from": ["Escherichia", "Shigella"],
      "notes": "VP positivity helps separate Enterobacter from MR-positive Enterobacterales."
    },
    {
      "field": "Citrate",
      "expected": "Positive",
      "distinguishes_from": ["Escherichia"],
      "notes": "Citrate utilization supports Enterobacter over E. coli."
    },
    {
      "field": "Motility",
      "expected": "Positive",
      "distinguishes_from": ["Klebsiella"],
      "notes": "Motility differentiates Enterobacter from typically non-motile Klebsiella."
    }
  ],

  "common_confusions": [
    {
      "genus": "Klebsiella",
      "reason": "Shared lactose fermentation and mucoid colony appearance can cause confusion."
    },
    {
      "genus": "Citrobacter",
      "reason": "Overlapping biochemical reactions including citrate positivity and sugar fermentation."
    }
  ],

  "when_to_question_identification": [
    "Non-motile isolate with strong capsule suggests Klebsiella.",
    "Indole-positive with MR-positive profile suggests Escherichia or Citrobacter.",
    "H2S production argues against Enterobacter."
  ],

  "recommended_next_tests": [
    {
      "test": "Indole test",
      "reason": "Useful for narrowing species-level identification."
    },
    {
      "test": "Motility testing",
      "reason": "Helps distinguish from Klebsiella."
    },
    {
      "test": "Molecular identification or MALDI-TOF",
      "reason": "Recommended due to biochemical overlap within Enterobacterales."
    }
  ],

  "supported_species": [
    "cloacae",
    "asburiae",
    "hormaechei",
    "kobei",
    "ludwigii"
  ]
}