data/rag/knowledge_base/Bacillus/anthracis.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Bacillus",
  "species": "anthracis",

  "overview": {
    "short": "Bacillus anthracis is a non-motile, encapsulated, Gram-positive spore-forming rod and the causative agent of anthrax.",
    "clinical_context": "A high-consequence pathogen requiring immediate public health notification."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Rods",
    "Motility": "Negative",
    "Capsule": "Positive",
    "Spore Formation": "Positive",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Large",
      "Non-haemolytic",
      "Ground-glass"
    ],
    "Oxygen Requirement": "Aerobic",
    "Growth Temperature": "35//37",
    "Catalase": "Positive",
    "Oxidase": "Variable",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Variable",
    "Methyl Red": "Variable",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Positive",
    "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": "Variable",
    "Lactose Fermentation": "Negative",
    "Sucrose Fermentation": "Negative",
    "Maltose Fermentation": "Variable",
    "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"
  },

  "species_markers": [
    {
      "field": "Motility",
      "value": "Negative",
      "importance": "critical",
      "notes": "Non-motility is a key discriminator from B. cereus group."
    },
    {
      "field": "Haemolysis",
      "value": "Negative",
      "importance": "critical",
      "notes": "Non-haemolytic colonies strongly suggest B. anthracis."
    },
    {
      "field": "Capsule",
      "value": "Positive",
      "importance": "critical",
      "notes": "Poly-D-glutamate capsule is a defining virulence factor."
    }
  ],

  "common_confusions": [
    {
      "species": "Bacillus cereus",
      "reason": "Close genetic relationship but differs in motility and haemolysis."
    }
  ],

  "when_to_question_identification": [
    "Any haemolysis excludes B. anthracis.",
    "Motility excludes B. anthracis.",
    "Pigment production argues against B. anthracis."
  ],

  "recommended_next_tests": [
    {
      "test": "Gamma phage susceptibility",
      "reason": "Highly specific for Bacillus anthracis.",
      "api_kit": "Not applicable (reference laboratory assay)"
    },
    {
      "test": "Capsule demonstration",
      "reason": "Confirms virulence-associated capsule."
    },
    {
      "test": "PCR for anthrax toxin genes",
      "reason": "Definitive confirmation in reference laboratories."
    }
  ]
}