Update data/rag/knowledge_base/Escherichia/fergusonii.json

data/rag/knowledge_base/Escherichia/fergusonii.json

@@ -1,48 +1,121 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Escherichia",
   "species": "fergusonii",
-  "full_name": "Escherichia fergusonii",
-  "clinical_significance": "A rare human pathogen causing UTIs, wound infections, bacteremia, and occasional gastrointestinal disease. Often isolated from animals and environmental sources. Frequently misidentified as atypical E. coli or Enterobacter due to its weaker lactose fermentation.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Lactose negative or late lactose fermenter; ONPG positive. Colonies may appear similar to non-fermenting E. coli.",
-    "biochemical": [
-      "Indole negative or weak",
-      "ONPG positive",
-      "Lysine decarboxylase positive",
-      "Citrate negative (important genus-level trait)",
-      "Gas from glucose variable",
-      "Motile",
-      "Urease negative"
-    ]
+
+  "overview": {
+    "short": "Escherichia fergusonii is a Gram-negative, facultatively anaerobic rod closely related to Escherichia coli.",
+    "clinical_context": "Occasionally isolated from human clinical specimens including wounds, urine, and bloodstream infections."
   },
-  "differentiation": {
-    "from close species": [
-      "Lactose negative but ONPG positive pattern differentiates from typical E. coli.",
-      "Citrate negative separates it from Enterobacter.",
-      "Indole negative and weaker LF distinguish from E. coli."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from other genera": [
-      "Lysine positive distinguishes from Citrobacter (lysine negative).",
-      "Motility distinguishes from Klebsiella."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Positive",
+    "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": [
-      "Limited data; may share adherence and iron acquisition genes with E. coli.",
-      "Potential zoonotic transmission."
+
+  "species_markers": [
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "More consistently positive than in E. coli."
+    },
+    {
+      "field": "Indole",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Helps separate E. fergusonii from most E. coli strains."
+    },
+    {
+      "field": "Sorbitol Fermentation",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Non-sorbitol fermentation supports differentiation from common E. coli."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Biochemical profile (ONPG+, citrate–, LF-variable)",
-      "Whole-genome sequencing for accurate classification"
+
+  "common_confusions": [
+    {
+      "species": "Escherichia coli",
+      "reason": "Very close biochemical and genetic relationship."
+    }
   ],
-  "treatment_notes": [
-      "Generally susceptible to common agents but resistance patterns variable.",
-      "No unique resistance mechanisms known compared to E. coli."
+
+  "when_to_question_identification": [
+    "Indole positivity suggests E. coli.",
+    "Rhamnose negativity weakens support for E. fergusonii.",
+    "Atypical sugar patterns require molecular confirmation."
   ],
-  "notes": "Common laboratory misidentification occurs due to overlapping biochemical features.",
-  "references": [
-      "Taxonomic studies describing E. fergusonii",
-      "Case reports of human infections"
+
+  "recommended_next_tests": [
+    {
+      "test": "Rhamnose fermentation",
+      "reason": "Useful discriminator from E. coli.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "Indole test",
+      "reason": "Excludes most E. coli strains.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable species-level differentiation.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}