Update data/rag/knowledge_base/Cedecea/davisae.json

data/rag/knowledge_base/Cedecea/davisae.json

@@ -1,50 +1,113 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Cedecea",
   "species": "davisae",
-  "full_name": "Cedecea davisae",
-  "clinical_significance": "The most frequently reported Cedecea species in human infections. Causes opportunistic infections such as bacteremia, pneumonia, cellulitis, wound infections, and UTIs, especially in elderly or immunocompromised patients. Known for intrinsic multidrug resistance.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative straight rods; motile.",
-    "culture": "Grows on MacConkey agar as NLF or weak LF colonies. May produce pinkish or slightly mucoid colonies. No pigment.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase positive",
-      "DNase positive",
-      "Lipase positive",
-      "ONPG variable",
-      "Urease negative",
-      "Indole negative",
-      "Intrinsic resistance to colistin and cephalothin",
-      "Variable lactose fermentation"
-    ]
+
+  "overview": {
+    "short": "Cedecea davisae is a rare, Gram-negative, facultatively anaerobic rod within the Enterobacterales.",
+    "clinical_context": "Occasionally isolated from opportunistic infections including bacteremia and respiratory infections, primarily in immunocompromised patients."
   },
-  "differentiation": {
-    "from close species": [
-      "C. davisae is the most common clinical species vs. C. lapagei (rarer).",
-      "Similar to Serratia but lipase positive and with unique resistance profile.",
-      "Higher frequency in bloodstream infections compared to C. lapagei."
+
+  "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": [
-      "Intrinsic colistin resistance helps distinguish from most Enterobacterales.",
-      "DNase + lipase positivity unique versus Enterobacter, Klebsiella, Citrobacter."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "30//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Positive",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Positive",
+    "Ornitihine Decarboxylase": "Positive",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "β-lactamases contributing to multidrug resistance",
-    "Efflux pumps",
-    "Biofilm formation",
-    "Potential for adherence to medical devices"
+
+  "species_markers": [
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key discriminator separating C. davisae from C. lapagei."
+    },
+    {
+      "field": "Lysine Decarboxylase",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Supports differentiation from some Enterobacter species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Cedecea lapagei",
+      "reason": "Closely related species with overlapping biochemical reactions."
+    },
+    {
+      "genus": "Enterobacter",
+      "reason": "Shared citrate and VP positivity may cause misidentification."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "DNase + lipase profile",
-    "Antimicrobial susceptibility showing intrinsic colistin resistance",
-    "16S sequencing if needed"
+
+  "when_to_question_identification": [
+    "Ornithine decarboxylase is negative.",
+    "Lactose fermentation is present.",
+    "Indole is positive."
   ],
-  "treatment_notes": "Infections can be difficult to treat due to resistance. Agents with activity may include carbapenems, fluoroquinolones, or TMP-SMX depending on isolate. Susceptibility testing required.",
-  "notes": "Frequently misidentified pre-MALDI era; now more frequently recognized.",
-  "references": [
-    "Cedecea davisae case reports",
-    "Rare Enterobacterales infection data"
+
+  "recommended_next_tests": [
+    {
+      "test": "Ornithine decarboxylase",
+      "reason": "Primary discriminator between Cedecea species.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable confirmation for rare Enterobacterales species."
+    }
   ]
-}
+}