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

data/rag/knowledge_base/Corynebacterium/genus.json

@@ -1,79 +1,147 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Corynebacterium",
-  "taxonomy": {
-    "family": "Corynebacteriaceae",
-    "order": "Corynebacteriales",
-    "class": "Actinobacteria",
-    "phylum": "Actinobacteriota"
+
+  "overview": {
+    "short": "Corynebacterium species are Gram-positive, non-spore-forming rods characterized by pleomorphic morphology and club-shaped cells.",
+    "clinical_context": "Includes both commensal skin flora and clinically significant pathogens, most notably Corynebacterium diphtheriae."
   },
-  "overview": "Corynebacterium is a genus of aerobic, Gram-positive, catalase-positive, non-spore-forming coryneform rods. While many species are part of normal human skin or mucosal flora, several are significant pathogens including Corynebacterium diphtheriae, Corynebacterium jeikeium, and Corynebacterium striatum. The group has diverse biochemical properties ranging from lipophilic, slow-growing strains to classic diphtheroid morphotypes.",
-  "key_traits": [
-    "Gram-positive coryneform rods ('Chinese letter' arrangement)",
-    "Non-motile",
-    "Catalase positive",
-    "Oxidase negative",
-    "Non-spore-forming",
-    "Some species lipophilic (require lipid supplementation)",
-    "Nitrate reduction variable",
-    "Urease variable",
-    "Non-acid-fast (weakly acid-fast in a few species)"
-  ],
-  "ecology": "Colonizers of human skin, respiratory mucosa, urogenital tract, and hospital surfaces. Environmental species inhabit water and soil. Lipophilic species prefer moist areas such as axilla and groin.",
-  "pathogenicity": "C. diphtheriae causes diphtheria via exotoxin expression. C. jeikeium and C. striatum are major opportunistic pathogens causing nosocomial infections, bacteremia, endocarditis, device infections, pneumonia, and wound infections—particularly in immunocompromised or hospitalized patients.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Catalase positive coryneform rods.",
-      "Non-motile, non-spore-forming.",
-      "Many species ferment glucose.",
-      "Lipophilic species show poor growth unless lipids added.",
-      "Urease and nitrate reactions help separate species."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar",
+      "Tellurite Agar"
     ],
-    "non_definitive_tests": [
-      "Colony morphology varies widely.",
-      "Gram stain can resemble other coryneform genera."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Cutibacterium (formerly Propionibacterium) are anaerobic; Corynebacterium are aerobic.",
-      "Dermabacter hominis is catalase positive but differs in fatty acid profile and is non-lipophilic.",
-      "Brevibacterium produce strong cheese-like odor and distinct pigmentation.",
-      "Trueperella are catalase negative and often β-hemolytic.",
-      "Nocardia are partially acid-fast and filamentous."
+    "Colony Morphology": [
+      "Dry",
+      "Grey",
+      "White",
+      "Irregular"
     ],
-    "key_rag_filters": [
-      "Aerobic coryneform rod + catalase positive → Corynebacterium vs Brevibacterium/Microbacterium.",
-      "Lipophilic slow growth → suggests C. jeikeium.",
-      "Multidrug-resistant diphtheroid → C. striatum or C. jeikeium.",
-      "Black/gray colonies + ELEK/PCR positive → C. diphtheriae."
-    ]
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Variable",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Variable",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Unknown"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Gram-positive coryneform rods in palisades",
-      "Catalase positivity",
-      "Non-hemolytic generally (except diphtheriae biotypes)",
-      "Variable growth depending on lipophilicity"
-    ],
-    "important_tests": [
-      "Nitrate reduction",
-      "Urease test",
-      "Lipid-dependence testing",
-      "Sugar fermentation patterns",
-      "MALDI-TOF MS",
-      "ELEK test for toxin detection"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS",
-      "PCR for tox gene (C. diphtheriae)",
-      "Biochemical profiling",
-      "Whole-genome sequencing for MDR strains"
-    ]
+
+  "field_notes": {
+    "Shape": "Often described as pleomorphic or club-shaped; may appear as short rods with palisading arrangements.",
+    "Haemolysis": "Highly species-dependent; toxigenic species may show weak haemolysis.",
+    "Urease": "Useful for separating non-diphtheriae Corynebacterium species."
   },
-  "notes": "Corynebacterium species range from harmless commensals to highly significant pathogens, requiring careful interpretation of clinical context.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Corynebacterium taxonomy literature",
-    "C. diphtheriae and MDR organism surveillance"
+
+  "key_differentiators": [
+    {
+      "field": "Catalase",
+      "expected": "Positive",
+      "distinguishes_from": ["Actinomyces", "Arcanobacterium"],
+      "notes": "Catalase positivity supports Corynebacterium over related Gram-positive rods."
+    },
+    {
+      "field": "Motility",
+      "expected": "Negative",
+      "distinguishes_from": ["Listeria"],
+      "notes": "Non-motility helps exclude Listeria species."
+    },
+    {
+      "field": "Tellurite Growth",
+      "expected": "Positive",
+      "distinguishes_from": ["Cutibacterium"],
+      "notes": "Tellurite reduction is characteristic of Corynebacterium diphtheriae."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Listeria",
+      "reason": "Similar Gram-positive rod morphology in clinical specimens."
+    },
+    {
+      "genus": "Arcanobacterium",
+      "reason": "Overlapping morphology and haemolytic behavior."
+    },
+    {
+      "genus": "Cutibacterium",
+      "reason": "Skin flora overlap in non-sterile samples."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Motility or tumbling motility suggests Listeria.",
+    "Strict anaerobic growth suggests Cutibacterium.",
+    "Oxidase positivity argues against Corynebacterium."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Catalase test",
+      "reason": "Confirms genus-level placement among Gram-positive rods.",
+      "api_kit": "API Coryne"
+    },
+    {
+      "test": "Urease test",
+      "reason": "Useful for species-level differentiation.",
+      "api_kit": "API Coryne"
+    },
+    {
+      "test": "Tox gene detection",
+      "reason": "Required when Corynebacterium diphtheriae is suspected.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable identification of non-diphtheriae Corynebacterium.",
+      "api_kit": "Not applicable"
+    }
+  ],
+
+  "supported_species": [
+    "diphtheriae",
+    "jeikeium",
+    "striatum"
   ]
-}
+}