Update data/rag/knowledge_base/Actinomyces/israelii.json

data/rag/knowledge_base/Actinomyces/israelii.json

@@ -1,44 +1,108 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Actinomyces",
   "species": "israelii",
-  "full_name": "Actinomyces israelii",
-  "clinical_significance": "Actinomyces israelii is the most common cause of human actinomycosis, including cervicofacial ('lumpy jaw'), thoracic, abdominal, and pelvic infections. It forms sulfur granules and causes chronic suppurative disease with sinus tracts.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive branching filamentous rods; densely filamentous in sulfur granules.",
-    "culture": "Slow-growing anaerobe with classic molar-tooth colonies on blood agar. No growth on aerobic plates.",
-    "biochemical": [
-      "Non–acid-fast",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Non-motile",
-      "Ferments glucose → produces lactic, acetic, succinic acids",
-      "Catalase variable",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Actinomyces israelii is a Gram-positive, non-spore-forming, filamentous rod classically associated with actinomycosis.",
+    "clinical_context": "Most common cause of cervicofacial actinomycosis, often presenting with chronic abscesses and draining sinus tracts containing sulfur granules."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More strongly associated with sulfur granules than A. naeslundii or A. odontolyticus.",
-      "Typically stricter anaerobe compared to A. naeslundii (which may show weak aerotolerance).",
-      "Colony morphology more strongly 'molar tooth' compared to smoother colonies of other species."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Nocardia is partially acid-fast; A. israelii is non–acid-fast.",
-      "Cutibacterium is non-filamentous and lacks sulfur granules.",
-      "Streptomyces is aerobic and environmental."
-    ]
+    "Colony Morphology": [
+      "White",
+      "Grey",
+      "Rough",
+      "Irregular"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "30//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Unknown",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Unknown",
+    "Ornithine Decarboxylase": "Unknown",
+    "Ornitihine Decarboxylase": "Unknown",
+    "Arginine dihydrolase": "Unknown",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Unknown",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Unknown",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Unknown",
+    "Gas Production": "Variable",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S rRNA sequencing",
-    "Histology demonstrating sulfur granules",
-    "Anaerobic growth with filamentous Gram stain"
+
+  "species_markers": [
+    {
+      "field": "Gelatin Hydrolysis",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Consistent gelatin hydrolysis supports A. israelii."
+    },
+    {
+      "field": "Lactose Fermentation",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Helps separate from oral Actinomyces species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Actinomyces naeslundii",
+      "reason": "Shared oral habitat and overlapping anaerobic growth characteristics."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Catalase positivity suggests aerobic actinomycetes.",
+    "Strong aerobic growth argues against A. israelii.",
+    "Acid-fast positivity suggests Nocardia."
   ],
-  "treatment_notes": "Highly susceptible to penicillin; therapy often prolonged (6–12 months) due to chronic nature of infection.",
-  "notes": "Primary species implicated in classic actinomycosis; frequently polymicrobial with other anaerobes.",
-  "references": [
-    "Manual of Clinical Microbiology.",
-    "Textbook of Oral Microbiology.",
-    "Actinomycosis clinical reviews."
+
+  "recommended_next_tests": [
+    {
+      "test": "Anaerobic culture",
+      "reason": "Required for optimal recovery and confirmation."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable species-level differentiation."
+    }
   ]
-}
+}