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

data/rag/knowledge_base/Corynebacterium/diphtheriae.json

@@ -5,8 +5,8 @@
   "species": "diphtheriae",
 
   "overview": {
-    "short": "Corynebacterium diphtheriae is a Gram-positive, non-motile rod capable of producing diphtheria toxin.",
-    "clinical_context": "Causes diphtheria, a toxin-mediated disease affecting the respiratory tract and skin."
+    "short": "Corynebacterium diphtheriae is a Gram-positive, non-motile, non-spore-forming rod capable of producing diphtheria toxin.",
+    "clinical_context": "The causative agent of diphtheria, a potentially fatal toxin-mediated disease affecting the upper respiratory tract and skin."
   },
 
   "expected_fields": {
@@ -22,8 +22,9 @@
       "Tellurite Agar"
     ],
     "Colony Morphology": [
-      "Dry",
       "Grey",
+      "White",
+      "Dry",
       "Irregular"
     ],
     "Oxygen Requirement": "Aerobic",
@@ -33,12 +34,36 @@
     "Indole": "Negative",
     "Urease": "Negative",
     "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
     "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
     "Glucose Fermentation": "Positive",
-    "Maltose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
     "Sucrose Fermentation": "Variable",
-    "Trehalose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
     "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
     "Pigment": "None",
     "Motility Type": "Unknown"
   },
@@ -51,33 +76,56 @@
       "notes": "Characteristic black colonies on tellurite-containing media."
     },
     {
-      "field": "Tox Gene",
+      "field": "Nitrate Reduction",
       "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports differentiation from some non-diphtheriae Corynebacterium."
+    },
+    {
+      "field": "tox Gene",
+      "value": "Present (toxigenic strains only)",
       "importance": "critical",
-      "notes": "Defines toxigenic strains responsible for clinical diphtheria."
+      "notes": "Presence of tox gene determines pathogenicity."
     }
   ],
 
   "common_confusions": [
     {
       "species": "Corynebacterium ulcerans",
-      "reason": "May also carry diphtheria toxin genes."
+      "reason": "Can also carry the tox gene and cause diphtheria-like illness."
+    },
+    {
+      "species": "Corynebacterium pseudotuberculosis",
+      "reason": "Biochemical overlap and related toxigenic potential."
     }
   ],
 
   "when_to_question_identification": [
-    "Absence of tellurite reduction argues against C. diphtheriae.",
-    "Non-toxigenic strains require molecular confirmation."
+    "Failure to reduce tellurite argues against C. diphtheriae.",
+    "Motility or spore formation excludes Corynebacterium.",
+    "Oxidase positivity suggests an alternative genus."
   ],
 
   "recommended_next_tests": [
+    {
+      "test": "tox gene PCR",
+      "reason": "Required to confirm toxigenic potential.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "Elek test",
+      "reason": "Phenotypic confirmation of diphtheria toxin production.",
+      "api_kit": "Not applicable"
+    },
     {
       "test": "API Coryne",
-      "reason": "Supports biochemical identification."
+      "reason": "Supports biochemical identification.",
+      "api_kit": "API Coryne"
     },
     {
-      "test": "PCR for tox gene",
-      "reason": "Required to confirm toxigenicity."
+      "test": "MALDI-TOF MS",
+      "reason": "Rapid and accurate species-level identification.",
+      "api_kit": "Not applicable"
     }
   ]
 }