Update data/rag/knowledge_base/Cronobacter/malonaticus.json

data/rag/knowledge_base/Cronobacter/malonaticus.json

@@ -1,48 +1,109 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Cronobacter",
   "species": "malonaticus",
-  "full_name": "Cronobacter malonaticus",
-  "clinical_significance": "Associated with severe infections in adults and neonates including septicemia, meningitis, and urinary tract infections. Often grouped in clinical relevance just after C. sakazakii.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Yellowish colonies, late lactose fermenter. Similar appearance to C. sakazakii.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase positive",
-      "α-glucosidase positive",
-      "Indole positive (key differentiator)",
-      "Dulcitol variable/negative",
-      "Esculin positive",
-      "Motile",
-      "Nitrate positive",
-      "Thermotolerant (growth at 45 °C)"
-    ]
+
+  "overview": {
+    "short": "Cronobacter malonaticus is a Gram-negative, facultatively anaerobic rod associated with opportunistic infections.",
+    "clinical_context": "More commonly isolated from adult infections than neonatal disease."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole positive distinguishes from C. sakazakii (indole negative).",
-      "Often associated with adult UTIs/bacteremia more than neonatal NEC.",
-      "Genotypic differences via fusA and rpoB sequencing."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "MacConkey Agar",
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Thermotolerant + α-glucosidase positive Eliminates Enterobacter and Klebsiella."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "6//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Positive",
+    "Methyl Red": "Variable",
+    "VP": "Positive",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Positive",
+    "Ornitihine Decarboxylase": "Positive",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Positive",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Positive",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Variable",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Invasion factors similar to sakazakii",
-    "Heat resistance enabling powdered food contamination",
-    "Biofilm formation on surfaces"
+
+  "species_markers": [
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Strong discriminator from C. sakazakii."
+    },
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports identification within the Cronobacter genus."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Cronobacter sakazakii",
+      "reason": "Closely related species with overlapping core biochemical profiles."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Indole reaction",
-    "fusA allele sequencing",
-    "PCR for species-specific markers"
+
+  "when_to_question_identification": [
+    "Rhamnose negativity suggests C. sakazakii.",
+    "Indole positivity suggests non-Cronobacter species."
   ],
-  "treatment_notes": "Treat based on susceptibilities; resistance patterns similar to C. sakazakii.",
-  "notes": "Likely underdiagnosed before widespread molecular identification.",
-  "references": [
-    "Cronobacter malonaticus clinical studies",
-    "Molecular epidemiology papers"
+
+  "recommended_next_tests": [
+    {
+      "test": "API 20E",
+      "reason": "Biochemical differentiation of Enterobacterales.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive Cronobacter species resolution.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}