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

data/rag/knowledge_base/Aggregatibacter/genus.json

@@ -1,80 +1,133 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Aggregatibacter",
-  "taxonomy": {
-    "family": "Pasteurellaceae",
-    "order": "Pasteurellales",
-    "class": "Gammaproteobacteria"
+
+  "overview": {
+    "short": "Aggregatibacter species are fastidious, Gram-negative coccobacilli within the Pasteurellaceae family, commonly associated with oral flora and endocarditis.",
+    "clinical_context": "Members of the HACEK group; most frequently implicated in infective endocarditis and periodontal disease."
   },
-  "overview": "Aggregatibacter is a genus of small, Gram-negative coccobacilli within the Pasteurellaceae family. They are facultatively anaerobic and fastidious, often requiring enriched media such as chocolate agar. Three species are clinically relevant: A. actinomycetemcomitans, A. aphrophilus, and A. segnis. They are well-known causes of periodontal disease and infective endocarditis as part of the HACEK group.",
-  "key_traits": [
-    "Gram-negative coccobacilli",
-    "Facultative anaerobes",
-    "Fastidious: improved growth on chocolate agar",
-    "Catalase positive (most species)",
-    "Oxidase variable",
-    "Non-motile",
-    "Do not grow in 6.5% NaCl",
-    "ONPG negative",
-    "Ferment glucose without gas",
-    "Associated with oral cavity and upper respiratory tract"
-  ],
-  "ecology": "Part of normal human oral and pharyngeal microbiota. Strongly associated with dental plaque, periodontal pockets, and juvenile periodontitis.",
-  "pathogenicity": "Major causes of endocarditis (as part of the HACEK group). A. actinomycetemcomitans is strongly associated with aggressive periodontitis. A. aphrophilus and A. segnis are opportunistic pathogens causing bacteremia, brain abscesses, and respiratory infections.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Glucose fermentation producing acid without gas.",
-      "Oxidase variable across species.",
-      "Catalase positive in most clinically relevant species.",
-      "ONPG negative.",
-      "No growth in 6.5% NaCl.",
-      "Slow and fastidious growth, often requiring CO₂ enrichment.",
-      "Satellite growth rarely observed (not a Haemophilus trait)."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate fermentation patterns vary and are unreliable for speciation.",
-      "Colonial morphology may vary widely between strains."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Haemophilus species often require V factor (NAD); Aggregatibacter does not.",
-      "Actinobacillus species are more animal-associated (except old taxonomy ties).",
-      "Pasteurella species are typically oxidase positive and often grow well on blood agar; Aggregatibacter is more fastidious.",
-      "Neisseria species are oxidase positive diplococci, not coccobacilli and non-fermenters differ from Pasteurellaceae fermentation profiles.",
-      "Capnocytophaga species are gliding, fusiform rods—not coccobacilli."
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Translucent"
     ],
-    "key_rag_filters": [
-      "Gram-negative coccobacilli + endocarditis → strongly push toward HACEK including Aggregatibacter.",
-      "No NAD requirement → favors Aggregatibacter over Haemophilus.",
-      "Oral source + localized aggressive periodontitis → A. actinomycetemcomitans.",
-      "Slow-growing GNR from blood cultures (HACEK profile) → strongly supports A. aphrophilus or A. segnis."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "35//37",
+    "Catalase": "Variable",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "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": "Variable",
+    "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": "Variable",
+    "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": [
-      "Small Gram-negative coccobacilli",
-      "Slow-growing on blood agar; better growth on chocolate",
-      "Oxidase variable",
-      "Catalase positive (usually)",
-      "Fermentation of glucose without gas"
-    ],
-    "important_tests": [
-      "Growth on chocolate agar with CO₂ enrichment",
-      "Catalase and oxidase tests",
-      "Carbohydrate fermentation profiles (supportive, not definitive)",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (high accuracy)",
-      "16S rRNA sequencing",
-      "Biochemical differentiation with caution due to variability",
-      "Clinical context (endocarditis, periodontitis)"
-    ]
+
+  "field_notes": {
+    "Shape": "Often described as coccobacilli microscopically; normalized here as Short Rods.",
+    "Growth Requirements": "Many species are fastidious and may require enriched media such as chocolate agar.",
+    "Catalase": "Catalase reactions vary by species."
   },
-  "notes": "Species formerly classified as Haemophilus are now placed in Aggregatibacter following genetic reclassification.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Taxonomic reviews of Pasteurellaceae",
-    "HACEK endocarditis literature"
+
+  "key_differentiators": [
+    {
+      "field": "Motility",
+      "expected": "Negative",
+      "distinguishes_from": ["Haemophilus"],
+      "notes": "Aggregatibacter species are non-motile, helping distinguish them from some Haemophilus species."
+    },
+    {
+      "field": "Oxidase",
+      "expected": "Negative",
+      "distinguishes_from": ["Neisseria", "Moraxella"],
+      "notes": "Oxidase negativity helps rule out oxidase-positive Gram-negative cocci."
+    },
+    {
+      "field": "Growth Characteristics",
+      "expected": "Fastidious",
+      "distinguishes_from": ["Enterobacterales"],
+      "notes": "Poor growth on MacConkey Agar helps separate Aggregatibacter from enteric Gram-negative rods."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Haemophilus",
+      "reason": "Shared family (Pasteurellaceae) and similar fastidious growth requirements."
+    },
+    {
+      "genus": "Cardiobacterium",
+      "reason": "Both are HACEK organisms associated with endocarditis."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Robust growth on MacConkey Agar argues against Aggregatibacter.",
+    "Oxidase positivity suggests Neisseria or Moraxella.",
+    "Strong lactose fermentation is inconsistent with Aggregatibacter."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Growth factor requirement testing",
+      "reason": "Helps distinguish Aggregatibacter from Haemophilus species."
+    },
+    {
+      "test": "Extended incubation",
+      "reason": "HACEK organisms often grow slowly and may require prolonged incubation."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Recommended due to fastidious growth and biochemical overlap."
+    }
+  ],
+
+  "supported_species": [
+    "actinomycetemcomitans",
+    "aphrophilus",
+    "segregatus"
   ]
-}
+}