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

data/rag/knowledge_base/Actinomyces/genus.json

@@ -1,78 +1,135 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Actinomyces",
-  "taxonomy": {
-    "family": "Actinomycetaceae",
-    "order": "Actinomycetales",
-    "class": "Actinobacteria"
+
+  "overview": {
+    "short": "Actinomyces species are Gram-positive, non-spore-forming, pleomorphic rods that commonly inhabit the human oral cavity, gastrointestinal tract, and female genital tract.",
+    "clinical_context": "Associated with chronic, suppurative infections (actinomycosis), often involving abscess formation and sinus tracts, typically in cervicofacial, thoracic, or abdominopelvic sites."
   },
-  "overview": "Actinomyces is a genus of Gram-positive, filamentous, branching, non–acid-fast rods that are facultatively anaerobic or strictly anaerobic depending on species. They are members of the normal oral, gastrointestinal, and genitourinary microbiota. Actinomyces species are most notable for causing actinomycosis, a chronic granulomatous infection characterized by abscesses, draining sinuses, and sulfur granules.",
-  "key_traits": [
-    "Gram-positive branching filamentous rods",
-    "Non–acid-fast (distinguishes from Nocardia)",
-    "Facultative or strict anaerobes",
-    "Non-motile",
-    "Catalase variable",
-    "Slow-growing, molar-tooth colonies on anaerobic media",
-    "Do not grow in 6.5% NaCl",
-    "ONPG negative",
-    "Produce sulfur granules in tissues",
-    "Associated with cervicofacial, thoracic, abdominal, and pelvic infections"
-  ],
-  "ecology": "Commensals of the human oropharynx, gastrointestinal tract, and female genital tract. Frequently associated with dental plaque, gingival crevices, tonsillar crypts, and IUD-associated infections.",
-  "pathogenicity": "Cause chronic suppurative infections with draining sinus tracts. Cervicofacial actinomycosis ('lumpy jaw') is most common. Polymicrobial synergy with anaerobes (e.g., Prevotella, Fusobacterium) enhances pathogenicity.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Ferment carbohydrates to produce lactic, succinic, and acetic acids.",
-      "Non–acid-fast and non-branching fragmentations distinguish them from Nocardia.",
-      "ONPG negative.",
-      "Do not tolerate 6.5% NaCl.",
-      "Catalase reactions vary by species but should not be used for identification.",
-      "Indole negative across common pathogenic 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"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate fermentation patterns vary and are not reliable for speciation.",
-      "Catalase variability does not reliably separate species."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Nocardia species are partially acid-fast and aerobic, whereas Actinomyces are non–acid-fast and facultatively anaerobic or anaerobic.",
-      "Streptomyces are aerobic, form aerial hyphae, and are environmental; Actinomyces are mucosal commensals.",
-      "Rothia species are coccoid or rod-shaped without extensive filamentation.",
-      "Cutibacterium (Propionibacterium) are anaerobic Gram-positive rods but do not form branching filaments.",
-      "Filamentous Candida species stain Gram-positive but show pseudohyphae with budding yeast forms."
+    "Colony Morphology": [
+      "White",
+      "Grey",
+      "Rough",
+      "Irregular"
     ],
-    "key_rag_filters": [
-      "Gram-positive branching filaments + anaerobic growth → strong push toward Actinomyces.",
-      "Non–acid-fast → rules out Nocardia and some aerobic actinomycetes.",
-      "Molar-tooth colonies → strongly supportive for Actinomyces.",
-      "Presence of sulfur granules → strongly supportive and highly discriminative."
-    ]
+    "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": "Variable",
+    "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": "Variable",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Variable",
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Branching Gram-positive rods appearing filamentous",
-      "Non–acid-fast",
-      "Slow anaerobic growth with molar-tooth colony morphology",
-      "Yellow sulfur granules in tissue specimens"
-    ],
-    "important_tests": [
-      "Gram stain of sulfur granules",
-      "Modified acid-fast stain to rule out Nocardia",
-      "Anaerobic culture on enriched media",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (preferred)",
-      "16S rRNA sequencing",
-      "Histopathology showing sulfur granules",
-      "Species-level carbohydrate fermentation patterns with caution"
-    ]
+
+  "field_notes": {
+    "Oxygen Requirement": "Many Actinomyces are best recovered under anaerobic or microaerophilic conditions, but may tolerate oxygen depending on species and culture conditions.",
+    "Colony Morphology": "Colonies are often irregular and may appear rough or granular; prolonged incubation can accentuate characteristic appearances.",
+    "Catalase": "Typically catalase negative, helping distinguish from aerobic actinomycetes."
   },
-  "notes": "Actinomyces infections are typically polymicrobial; isolation may require prolonged anaerobic incubation. Species identification is best performed with MALDI-TOF or sequencing.",
-  "references": [
-    "Manual of Clinical Microbiology, 12th Edition.",
-    "Koneman’s Diagnostic Microbiology.",
-    "Recent reviews on actinomycosis pathology."
+
+  "key_differentiators": [
+    {
+      "field": "Gram Stain",
+      "expected": "Positive",
+      "distinguishes_from": ["Actinobacillus", "Aggregatibacter"],
+      "notes": "Gram-positive morphology separates Actinomyces from Gram-negative oral flora."
+    },
+    {
+      "field": "Motility",
+      "expected": "Negative",
+      "distinguishes_from": ["Bacillus", "Listeria"],
+      "notes": "Non-motility supports Actinomyces over motile Gram-positive rods."
+    },
+    {
+      "field": "Spore Formation",
+      "expected": "Negative",
+      "distinguishes_from": ["Bacillus", "Clostridium"],
+      "notes": "Non-spore forming supports Actinomyces in chronic abscess settings."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Nocardia",
+      "reason": "Both can present as branching Gram-positive rods and cause chronic infections."
+    },
+    {
+      "genus": "Corynebacterium",
+      "reason": "Overlapping Gram-positive rod morphology may confuse if branching is not described."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Strong aerobic growth with catalase positivity suggests Nocardia or other aerobic actinomycetes.",
+    "Spore formation suggests Bacillus or Clostridium rather than Actinomyces.",
+    "Oxidase positivity argues against Actinomyces."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Anaerobic incubation",
+      "reason": "Improves recovery and supports identification consistent with Actinomyces."
+    },
+    {
+      "test": "Acid fast",
+      "reason": "Helps distinguish Actinomyces (typically non–acid fast) from Nocardia (often partially acid fast)."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred for reliable genus/species identification due to phenotypic overlap."
+    }
+  ],
+
+  "supported_species": [
+    "israelii",
+    "naeslundii",
+    "viscosus",
+    "odontolyticus",
+    "meyeri"
   ]
-}
+}