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

data/rag/knowledge_base/Cardiobacterium/genus.json

@@ -1,76 +1,128 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Cardiobacterium",
-  "taxonomy": {
-    "family": "Cardiobacteriaceae",
-    "order": "Neisseriales",
-    "class": "Gammaproteobacteria",
-    "phylum": "Proteobacteria"
+
+  "overview": {
+    "short": "Cardiobacterium species are Gram-negative, facultatively anaerobic rods belonging to the HACEK group of organisms.",
+    "clinical_context": "Primarily associated with subacute infective endocarditis, often in patients with underlying valvular disease."
   },
-  "overview": "Cardiobacterium is a genus of slow-growing, fastidious, capnophilic Gram-negative bacilli that belongs to the HACEK group. These organisms are part of the normal human oropharyngeal flora but are notorious causes of infective endocarditis. The two recognized species associated with humans are Cardiobacterium hominis and Cardiobacterium valvarum.",
-  "key_traits": [
-    "Pleomorphic Gram-negative rods (may appear as curved, filamentous, or in rosette clusters)",
-    "Oxidase positive",
-    "Catalase negative",
-    "Indole positive (important genus marker)",
-    "Capnophilic (require or prefer CO₂-enriched atmosphere)",
-    "Slow-growing on blood/chocolate agar (2–5 days)",
-    "Non-motile",
-    "Fermentation of certain sugars (species-dependent)",
-    "Do not grow in 6.5% NaCl",
-    "ONPG negative"
-  ],
-  "ecology": "Normal inhabitants of the human oropharynx. Transmission to bloodstream is usually due to mucosal disruption or dental manipulation.",
-  "pathogenicity": "Primarily associated with infective endocarditis, especially subacute native-valve disease. May cause bacteremia, vascular infections, and rarely soft tissue infections. HACEK organisms including Cardiobacterium have a predilection for cardiac tissues.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Indole positivity is characteristic.",
-      "Oxidase positive and catalase negative profile.",
-      "Capnophilic growth requirement.",
-      "Slow-growing: colonies may take several days to appear.",
-      "Pleomorphism and rosette formation are notable on Gram stain."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "non_definitive_tests": [
-      "Sugar fermentation tests have limited consistency.",
-      "Automated ID systems may misidentify as Haemophilus or Aggregatibacter."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Haemophilus species require X/V factors; Cardiobacterium does not.",
-      "Aggregatibacter aphrophilus is catalase negative and oxidase variable but not indole positive.",
-      "Kingella are β-hemolytic and oxidase positive but indole negative.",
-      "Eikenella corrodes agar and is bleach-odor positive; Cardiobacterium does neither.",
-      "Neisseria are diplococci, not pleomorphic rods."
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Grey"
     ],
-    "key_rag_filters": [
-      "Subacute endocarditis + Gram-negative pleomorphic rods → HACEK; indole positive strongly supports Cardiobacterium.",
-      "Rosette-forming Gram-negative rods → highly suggestive of Cardiobacterium hominis.",
-      "CO₂-dependent slow growth pushes away from Enterobacterales."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "35//37",
+    "Catalase": "Negative",
+    "Oxidase": "Positive",
+    "Indole": "Positive",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "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": [
-      "Pleomorphic Gram-negative rods, often in rosettes",
-      "Slow growth on blood/chocolate agar",
-      "Oxidase positive, catalase negative, indole positive",
-      "Enhanced growth in CO₂"
-    ],
-    "important_tests": [
-      "Indole test",
-      "Oxidase test",
-      "CO₂-dependent culture",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS",
-      "16S rRNA sequencing",
-      "PCR for HACEK organisms"
-    ]
+
+  "field_notes": {
+    "Oxidase": "Consistently positive, supporting differentiation from many Enterobacterales.",
+    "Indole": "Positive reaction is characteristic of the genus.",
+    "Growth": "Slow-growing organism; colonies may take several days to appear."
   },
-  "notes": "Cardiobacterium species rarely cause disease outside endocarditis. Their pleomorphism can mimic Haemophilus or even gram-variable organisms.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "HACEK endocarditis literature",
-    "Cardiobacterium species genomic studies"
+
+  "key_differentiators": [
+    {
+      "field": "Oxidase",
+      "expected": "Positive",
+      "distinguishes_from": ["Enterobacter", "Escherichia"],
+      "notes": "Oxidase positivity helps separate Cardiobacterium from Enterobacterales."
+    },
+    {
+      "field": "Indole",
+      "expected": "Positive",
+      "distinguishes_from": ["Aggregatibacter"],
+      "notes": "Indole positivity supports Cardiobacterium within the HACEK group."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Aggregatibacter",
+      "reason": "Both are HACEK organisms with similar clinical presentations."
+    },
+    {
+      "genus": "Kingella",
+      "reason": "Shared fastidious growth and Gram-negative rod morphology."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Oxidase-negative isolate.",
+    "Rapid growth on routine media.",
+    "Absence of indole production."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Oxidase test",
+      "reason": "Confirms oxidase positivity typical of Cardiobacterium.",
+      "api_kit": "API NH"
+    },
+    {
+      "test": "Indole test",
+      "reason": "Supports genus-level identification.",
+      "api_kit": "API NH"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive identification of fastidious HACEK organisms."
+    }
+  ],
+
+  "supported_species": [
+    "hominis",
+    "valvarum"
   ]
-}
+}