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

data/rag/knowledge_base/Corynebacterium/jeikeium.json

@@ -1,50 +1,110 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Corynebacterium",
   "species": "jeikeium",
-  "full_name": "Corynebacterium jeikeium",
-  "clinical_significance": "A major opportunistic Corynebacterium species causing bacteremia, endocarditis, device-related infections, and severe infections in neutropenic and immunocompromised patients. Known for high intrinsic multidrug resistance and strong lipophilicity.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive coryneform rods; often uniform and slender.",
-    "culture": "Lipophilic—requires lipid-enriched media for robust growth (e.g., Tween 80). Small, dry colonies. Slow-growing.",
-    "biochemical": [
-      "Catalase positive",
-      "Urease negative",
-      "Nitrate negative",
-      "Non-motile",
-      "Non-fermentative or weak fermenter",
-      "Strong lipophilicity is characteristic"
-    ]
+
+  "overview": {
+    "short": "Corynebacterium jeikeium is a Gram-positive, non-motile, non-fermentative rod associated with multidrug-resistant hospital infections.",
+    "clinical_context": "Primarily causes bloodstream and device-associated infections in immunocompromised or hospitalized patients."
   },
-  "differentiation": {
-    "from close species": [
-      "Lipophilicity is a hallmark (no growth on standard media without lipids).",
-      "Highly MDR—frequently resistant to β-lactams, macrolides, aminoglycosides, and tetracyclines.",
-      "Different from C. striatum, which is non-lipophilic and grows faster."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Resembles Cutibacterium morphologically but differs by aerobic metabolism.",
-      "Distinguished from Dermabacter by lipophilicity and resistance pattern."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Dry"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Positive",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Negative",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Negative",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Unknown"
   },
-  "virulence_factors": [
-    "Biofilm formation on devices",
-    "Intrinsic multidrug resistance genes",
-    "Skin colonization in hospitalized patients"
+
+  "species_markers": [
+    {
+      "field": "NaCl Tolerant (>=6%)",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "One of the most useful discriminators among non-diphtheriae Corynebacterium."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Biochemical inertness supports identification."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Lipid-dependent growth test",
-    "16S rRNA sequencing for confirmation in MDR outbreak settings"
+
+  "common_confusions": [
+    {
+      "species": "Corynebacterium striatum",
+      "reason": "Shared hospital ecology and resistance patterns."
+    }
   ],
-  "treatment_notes": [
-    "Vancomycin is the treatment of choice.",
-    "Daptomycin and linezolid effective alternatives.",
-    "β-lactams generally ineffective due to MDR."
+
+  "when_to_question_identification": [
+    "Glucose or maltose fermentation suggests alternative Corynebacterium species.",
+    "NaCl intolerance argues against C. jeikeium."
   ],
-  "notes": "Major cause of bloodstream infections in cancer centers and ICUs.",
-  "references": [
-    "Corynebacterium jeikeium MDR studies",
-    "Hospital outbreak reports",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "API Coryne",
+      "reason": "Primary biochemical identification system."
+    },
+    {
+      "test": "Antimicrobial susceptibility testing",
+      "reason": "Critical due to frequent multidrug resistance."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Most reliable species-level identification."
+    }
   ]
-}
+}