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

data/rag/knowledge_base/Escherichia/coli.json

@@ -1,57 +1,125 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Escherichia",
   "species": "coli",
-  "full_name": "Escherichia coli",
-  "clinical_significance": "One of the most important human pathogens, responsible for urinary tract infections, sepsis, intra-abdominal infections, neonatal meningitis, and diarrheal illnesses. Includes multiple diarrheagenic pathotypes (ETEC, EPEC, EHEC/STEC, EAEC, EIEC, DAEC). Also a major agent of community- and hospital-acquired infections.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative rods, motile (most strains).",
-    "culture": "Strong lactose fermenter; dry or mucoid pink colonies on MacConkey; β-hemolysis possible on blood agar (not universal).",
-    "biochemical": [
-      "Indole positive",
-      "Citrate negative",
-      "ONPG positive",
-      "Lysine decarboxylase positive",
-      "Motile (exceptions: EIEC-like strains)",
-      "Urease negative",
-      "Gas from glucose positive",
-      "Nitrate reduction positive"
-    ]
+
+  "overview": {
+    "short": "Escherichia coli is a Gram-negative, facultatively anaerobic rod that is a dominant member of the human gut microbiota and a leading cause of extraintestinal infections.",
+    "clinical_context": "Responsible for urinary tract infections, sepsis, neonatal meningitis, and multiple diarrheagenic syndromes."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole positive LF → classic E. coli pattern.",
-      "Shigella are non-motile and lysine negative.",
-      "Citrobacter are citrate positive or lysine negative.",
-      "Klebsiella are non-motile and urease positive."
+
+  "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": [
-      "Citrate negativity strongly distinguishes from Enterobacter and Klebsiella.",
-      "Gas from glucose differentiates from many Shigella."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Positive",
+    "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": "Positive",
+    "Ornitihine Decarboxylase": "Positive",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Positive",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Variable",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Positive",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-      "FimH adhesins (UPEC)",
-      "Shiga toxin (STEC)",
-      "LT/ST enterotoxins (ETEC)",
-      "Intimin (EPEC/EHEC)",
-      "Invasion plasmid antigens (EIEC)",
-      "Capsular polysaccharide (K1 capsule in neonatal meningitis)",
-      "Hemolysin and siderophores"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Classic feature of E. coli, though rare indole-negative strains exist."
+    },
+    {
+      "field": "Lactose Fermentation",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Rapid lactose fermentation on MacConkey Agar is characteristic."
+    },
+    {
+      "field": "Citrate",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Separates E. coli from Enterobacter and Citrobacter."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "PCR for virulence genes (stx, eae, ipaH, LT/ST, aggR)",
-      "Serotyping for O:H antigens",
-      "Whole-genome sequencing for outbreaks"
+
+  "common_confusions": [
+    {
+      "genus": "Shigella",
+      "reason": "Genetically nested within E. coli; biochemical differentiation may be subtle."
+    },
+    {
+      "species": "Escherichia albertii",
+      "reason": "Biochemically similar but typically indole negative and less motile."
+    }
   ],
-  "treatment_notes": [
-      "UTIs often treated with nitrofurantoin, TMP-SMX, fosfomycin, or fluoroquinolones (resistance varies).",
-      "Avoid antibiotics in STEC due to HUS risk.",
-      "ESBL- and carbapenemase-producing strains increasingly common."
+
+  "when_to_question_identification": [
+    "Indole negativity suggests non-coli Escherichia species.",
+    "Citrate positivity argues against E. coli.",
+    "Non-lactose fermenting isolates require confirmation."
   ],
-  "notes": "E. coli is genetically diverse; WGS is the gold standard for pathotype assignment.",
-  "references": [
-      "E. coli pathotype literature",
-      "Global AMR surveillance data"
+
+  "recommended_next_tests": [
+    {
+      "test": "Indole test",
+      "reason": "Primary discriminator at species level.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "Sorbitol fermentation",
+      "reason": "Useful for identifying O157:H7 variants.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Gold standard for routine species identification.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}