data/rag/knowledge_base/Brucella/genus.json

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

  "overview": {
    "short": "Brucella species are small, Gram-negative, non-motile coccobacilli that are facultative intracellular pathogens.",
    "clinical_context": "Causes brucellosis, a zoonotic infection transmitted via animals or unpasteurised dairy products, often presenting as a systemic febrile illness."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Short Rods",
    "Motility": "Negative",
    "Capsule": "Negative",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar",
      "Chocolate Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Smooth",
      "Convex",
      "Translucent"
    ],
    "Oxygen Requirement": "Aerobic",
    "Growth Temperature": "35//37",
    "Catalase": "Positive",
    "Oxidase": "Positive",
    "Indole": "Negative",
    "Urease": "Positive",
    "Citrate": "Negative",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Variable",
    "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": "Negative",
    "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": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "field_notes": {
    "Urease": "Rapid urease positivity is a key genus-defining feature.",
    "Oxidase": "Oxidase positivity helps distinguish Brucella from many Enterobacterales.",
    "Growth": "Growth is slow and colonies may take several days to appear."
  },

  "key_differentiators": [
    {
      "field": "Urease",
      "expected": "Positive",
      "distinguishes_from": ["Francisella", "Haemophilus"],
      "notes": "Rapid urease activity is characteristic of Brucella."
    },
    {
      "field": "Glucose Fermentation",
      "expected": "Negative",
      "distinguishes_from": ["Enterobacterales"],
      "notes": "Brucella species are non-fermenters."
    },
    {
      "field": "Motility",
      "expected": "Negative",
      "distinguishes_from": ["Ochrobactrum"],
      "notes": "Non-motility helps differentiate from closely related genera."
    }
  ],

  "common_confusions": [
    {
      "genus": "Ochrobactrum",
      "reason": "Phylogenetically related with overlapping oxidase and urease reactions."
    },
    {
      "genus": "Haemophilus",
      "reason": "Small Gram-negative coccobacilli with slow growth."
    }
  ],

  "when_to_question_identification": [
    "Motility argues against Brucella.",
    "Carbohydrate fermentation suggests an alternative genus.",
    "Poor growth without CO₂ supplementation may require reassessment."
  ],

  "recommended_next_tests": [
    {
      "test": "Urease (rapid)",
      "reason": "Strong early indicator of Brucella.",
      "api_kit": "API NH"
    },
    {
      "test": "Oxidase and catalase",
      "reason": "Supports genus-level identification.",
      "api_kit": "API NH"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Preferred for rapid identification with appropriate biosafety precautions."
    },
    {
      "test": "PCR or reference laboratory confirmation",
      "reason": "Required due to biosafety risk and clinical significance."
    }
  ],

  "supported_species": [
    "abortus",
    "melitensis",
    "suis"
  ]
}