Update data/rag/knowledge_base/Enterococcus/faecium.json

data/rag/knowledge_base/Enterococcus/faecium.json

@@ -1,53 +1,115 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Enterococcus",
   "species": "faecium",
-  "full_name": "Enterococcus faecium",
-  "clinical_significance": "A highly antimicrobial-resistant Enterococcus species and major cause of hospital-associated infections. Vancomycin-resistant E. faecium (VREfm) carrying VanA/VanB genes is a critical public health concern. Causes bacteremia, endocarditis, intra-abdominal infection, and UTIs.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive cocci in chains.",
-    "culture": "Typically non-hemolytic or α-hemolytic.",
-    "biochemical": [
-      "PYR positive",
-      "Bile esculin positive",
-      "Growth in 6.5% NaCl",
-      "Arabinose positive (key for differentiation)",
-      "Motility negative",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Enterococcus faecium is a Gram-positive, facultatively anaerobic coccus notable for antimicrobial resistance and healthcare-associated infections.",
+    "clinical_context": "Frequently associated with bacteremia, urinary tract infections, and hospital-acquired infections, particularly vancomycin-resistant strains (VRE)."
   },
-  "differentiation": {
-    "from close species": [
-      "Arabinose positive → major differentiator vs E. faecalis (arabinose–).",
-      "Ampicillin resistance common due to altered PBP5.",
-      "Primary species associated with VanA/VanB vancomycin resistance."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Bile Esculin Agar"
     ],
-    "from other genera": [
-      "Growth in NaCl + bile esculin + PYR eliminates Streptococcus.",
-      "Gas-negative glucose fermentation differentiates from Leuconostoc (gas-producing)."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Positive",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose 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": "None"
   },
-  "virulence_factors": [
-      "Biofilm formation",
-      "Surface adhesins (Esp)",
-      "Vancomycin resistance genes (VanA/VanB)",
-      "Multidrug efflux pumps",
-      "Altered PBP5 conferring β-lactam resistance"
+
+  "species_markers": [
+    {
+      "field": "Arginine dihydrolase",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Primary discriminator separating E. faecium from E. faecalis."
+    },
+    {
+      "field": "Mannitol Fermentation",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "E. faecium typically does not ferment mannitol."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Arabinose fermentation test",
-      "VanA/VanB PCR for VRE",
-      "WGS for outbreak detection"
+
+  "common_confusions": [
+    {
+      "species": "Enterococcus faecalis",
+      "reason": "Shared genus traits and overlapping sugar fermentation profiles."
+    }
   ],
-  "treatment_notes": [
-      "Ampicillin usually ineffective due to high-level resistance.",
-      "For VRE: linezolid or daptomycin are preferred agents.",
-      "Daptomycin high-dose therapy required for bacteremia.",
-      "Tigecycline may be active for intra-abdominal infections."
+
+  "when_to_question_identification": [
+    "Arginine dihydrolase positivity suggests E. faecalis.",
+    "Strong mannitol fermentation is inconsistent.",
+    "Unexpected antimicrobial susceptibility patterns."
   ],
-  "notes": "A leading cause of nosocomial bacteremia in many regions.",
-  "references": [
-      "Vancomycin-resistant Enterococcus surveillance",
-      "Hospital outbreak genomics"
+
+  "recommended_next_tests": [
+    {
+      "test": "Arginine dihydrolase",
+      "reason": "Key biochemical discriminator from E. faecalis.",
+      "api_kit": "API Strep"
+    },
+    {
+      "test": "Vancomycin susceptibility testing",
+      "reason": "Critical due to frequent resistance in E. faecium.",
+      "api_kit": "VITEK 2 GP"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate species-level identification.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}