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

data/rag/knowledge_base/Actinomyces/naeslundii.json

@@ -1,42 +1,106 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Actinomyces",
   "species": "naeslundii",
-  "full_name": "Actinomyces naeslundii",
-  "clinical_significance": "Actinomyces naeslundii is common in the oral cavity and is associated with dental plaque formation, root surface caries, and opportunistic infections such as cervicofacial abscesses. It is less strongly associated with sulfur granules than A. israelii.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive branching rods with less dense filamentation than A. israelii.",
-    "culture": "Slow-growing; may show slightly smoother colonies than classic molar-tooth morphology.",
-    "biochemical": [
-      "Non–acid-fast",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Non-motile",
-      "Ferments glucose and other carbohydrates",
-      "Catalase variable",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Actinomyces naeslundii is a Gram-positive, non-spore-forming rod commonly found in the human oral cavity.",
+    "clinical_context": "Associated with dental plaque, root caries, and occasional invasive infections."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Less strict anaerobe than A. israelii; may survive brief oxygen exposure.",
-      "Distinguished from A. odontolyticus by fermentation profiles and colony morphology.",
-      "A. naeslundii is strongly associated with dental plaque ecology."
+
+  "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": [
-      "Branching morphology differentiates from Cutibacterium.",
-      "Non–acid-fast nature separates it from Nocardia."
-    ]
+    "Colony Morphology": [
+      "White",
+      "Grey",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "30//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Variable",
+    "Urease": "Variable",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Unknown",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Unknown",
+    "Ornithine Decarboxylase": "Unknown",
+    "Ornitihine Decarboxylase": "Unknown",
+    "Arginine dihydrolase": "Unknown",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Positive",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Unknown",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Unknown",
+    "Trehalose Fermentation": "Positive",
+    "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",
-    "Carbohydrate fermentation patterns (supplementary)",
-    "Colony morphology and oral origin"
+
+  "species_markers": [
+    {
+      "field": "Esculin Hydrolysis",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Useful discriminator among oral Actinomyces."
+    },
+    {
+      "field": "Lactose Fermentation",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Helps differentiate from A. israelii."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Actinomyces odontolyticus",
+      "reason": "Both are oral species with overlapping sugar fermentation patterns."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Gelatin hydrolysis positivity suggests other Actinomyces species.",
+    "Strict anaerobiosis suggests A. israelii."
   ],
-  "treatment_notes": "Penicillin susceptible; clinical management often involves dental intervention and drainage.",
-  "notes": "Common commensal of the oral cavity; contributes to early dental plaque formation.",
-  "references": [
-    "Oral microbiology texts.",
-    "Manual of Clinical Microbiology."
+
+  "recommended_next_tests": [
+    {
+      "test": "Esculin hydrolysis",
+      "reason": "Key species-level discriminator."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate differentiation among oral Actinomyces."
+    }
   ]
-}
+}