Update data/rag/knowledge_base/Brucella/genus.json

data/rag/knowledge_base/Brucella/genus.json

@@ -1,78 +1,140 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Brucella",
-  "taxonomy": {
-    "family": "Brucellaceae",
-    "order": "Hyphomicrobiales",
-    "class": "Alphaproteobacteria",
-    "phylum": "Proteobacteria"
+
+  "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."
   },
-  "overview": "Brucella is a genus of small, non-motile, Gram-negative coccobacilli that cause brucellosis, a systemic zoonotic infection acquired through contact with infected animals or consumption of unpasteurized dairy products. Brucella species are facultative intracellular pathogens that survive within macrophages, enabling chronic infections. They are highly infectious and require biosafety precautions.",
-  "key_traits": [
-    "Gram-negative coccobacilli (faintly staining)",
-    "Non-motile",
-    "Facultative intracellular pathogens",
-    "Strict aerobes with slow growth",
-    "Oxidase positive",
-    "Catalase positive",
-    "Rapid urease positive (within minutes)",
-    "Do not grow in 6.5% NaCl",
-    "ONPG negative",
-    "No carbohydrate fermentation",
-    "Grow poorly on standard media; enriched media and prolonged incubation often required"
-  ],
-  "ecology": "Brucella species infect domestic and wild animals—cattle, goats, sheep, pigs, dogs—serving as reservoirs. Transmission to humans occurs via unpasteurized dairy, contact with animal tissues, inhalation, or laboratory exposure.",
-  "pathogenicity": "Causes brucellosis, characterized by undulating fever, night sweats, malaise, lymphadenopathy, hepatosplenomegaly, arthritis, and chronic systemic disease. Can cause focal complications including osteomyelitis, neurobrucellosis, and endocarditis. Species differ in host preference and disease severity.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Oxidase positive.",
-      "Catalase positive.",
-      "Rapid urease positivity (major discriminating feature).",
-      "H2S production species dependent.",
-      "Non-fermentative and non-motile.",
-      "Very slow growth, often requiring 3–7 days or more."
+
+  "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"
     ],
-    "non_definitive_tests": [
-      "Gram stain may be faint and mistaken for other small GNRs.",
-      "Automated identification systems frequently misidentify Brucella as Ochrobactrum unless BSL protocols are used."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Bartonella spp. are oxidase negative and fastidious, whereas Brucella is oxidase positive and grows better on blood/chocolate agar.",
-      "Francisella tularensis is cysteine-requiring and oxidase negative; Brucella is oxidase positive and urease positive.",
-      "Coxiella burnetii is obligately intracellular and cannot grow on routine media.",
-      "Ochrobactrum anthropi may resemble Brucella biochemically but is motile and less urease rapid."
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Convex",
+      "Translucent"
     ],
-    "key_rag_filters": [
-      "Undulating fever + animal or unpasteurized dairy exposure → strong Brucella signal.",
-      "Rapid urease positivity → strong push toward Brucella.",
-      "Faint Gram-negative coccobacilli + slow growth → Brucella or Francisella; oxidase positivity distinguishes Brucella.",
-      "Laboratory exposure risk → flag Brucella in RAG logic for safety."
-    ]
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Faint Gram-negative coccobacilli",
-      "Slow-growing pinpoint colonies on enriched media",
-      "Positive oxidase, catalase, urease",
-      "Blood cultures may require extended incubation"
-    ],
-    "important_tests": [
-      "Serology (standard agglutination test, ELISA)",
-      "PCR on blood or tissue",
-      "Prolonged blood culture (up to 30 days in slow cases)",
-      "Bone marrow culture (highest yield)"
-    ],
-    "confirmation_methods": [
-      "PCR targeting bcsp31 or IS711",
-      "MALDI-TOF MS in BSL-3 environment",
-      "Biochemical panel: oxidase +, catalase +, urease rapid"
-    ]
+
+  "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."
   },
-  "notes": "Brucella is a high-risk laboratory pathogen; any suspected isolate must trigger biosafety protocols.",
-  "references": [
-    "CDC Brucellosis Guidelines",
-    "Manual of Clinical Microbiology",
-    "WHO Brucellosis Control Reports"
+
+  "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"
   ]
-}
+}