Update data/rag/knowledge_base/Enterobacter/genus.json

data/rag/knowledge_base/Enterobacter/genus.json

@@ -1,76 +1,135 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Enterobacter",
-  "taxonomy": {
-    "family": "Enterobacteriaceae",
-    "order": "Enterobacterales",
-    "class": "Gammaproteobacteria",
-    "phylum": "Proteobacteria"
+
+  "overview": {
+    "short": "Enterobacter species are Gram-negative, facultatively anaerobic rods within the Enterobacterales, commonly isolated from clinical and environmental sources.",
+    "clinical_context": "Often recovered from opportunistic infections including urinary tract, respiratory, and bloodstream infections."
   },
-  "overview": "Enterobacter is a genus of motile, Gram-negative, facultatively anaerobic bacilli associated with human and environmental microbiota. Many species belong to the Enterobacter cloacae complex (ECC), which is responsible for a major portion of healthcare-associated infections. Enterobacter species commonly harbor inducible AmpC β-lactamases and may acquire ESBLs or carbapenemases, making them significant nosocomial pathogens.",
-  "key_traits": [
-    "Gram-negative rods",
-    "Motile (peritrichous flagella)",
-    "Lactose fermenting or late-lactose fermenting",
-    "ONPG positive (β-galactosidase)",
-    "Citrate positive",
-    "Lysine decarboxylase positive",
-    "Ornithine decarboxylase positive (most ECC species)",
-    "Indole negative (species dependent)",
-    "Gas production from glucose (variable)",
-    "Nitrate reduction positive"
-  ],
-  "ecology": "Widely present in soil, plants, food, water, and hospital environments. Frequently colonize the human gastrointestinal tract.",
-  "pathogenicity": "Enterobacter species cause a broad range of infections including UTIs, pneumonia, bacteremia, intra-abdominal infections, wound infections, and device-related infections. ECC species, especially E. hormaechei, are major causes of multidrug-resistant outbreaks in hospitals and ICUs due to inducible AmpC and plasmid-mediated carbapenemase genes.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Motile, lactose fermenting, ONPG positive Enterobacterales.",
-      "Citrate positive, lysine positive (important discrimination from Citrobacter).",
-      "Ornithine decarboxylase positive (most species).",
-      "Indole usually negative except rare strains of E. asburiae or E. cloacae."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Variable",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "MacConkey Agar",
+      "Blood Agar"
     ],
-    "non_definitive_tests": [
-      "Biochemical panels often misidentify ECC members due to overlapping results.",
-      "MALDI-TOF required for reliable species-level resolution."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Klebsiella: non-motile; Enterobacter are motile.",
-      "Citrobacter: lysine negative vs lysine positive Enterobacter.",
-      "Serratia: DNase positive (Serratia) vs DNase negative (Enterobacter).",
-      "Cronobacter: thermotolerant and α-glucosidase positive; Enterobacter is not.",
-      "Pantoea: yellow pigmented and triple-decarboxylase negative."
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
     ],
-    "key_rag_filters": [
-      "Motile LF Enterobacterales + ONPG positive → Enterobacter / Klebsiella / Citrobacter. Check motility and lysine.",
-      "AmpC hyperproduction + hospital cluster → strongly Enterobacter cloacae complex.",
-      "Ornithine positive eliminates Citrobacter and many Klebsiella."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Variable",
+    "Urease": "Variable",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "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": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Variable",
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Pink lactose fermenting colonies on MacConkey",
-      "Motile Gram-negative rods",
-      "Citrate positive, ONPG positive",
-      "Lysine and ornithine positive"
-    ],
-    "important_tests": [
-      "Lysine and ornithine decarboxylase tests",
-      "Citrate utilization",
-      "Indole test",
-      "AmpC detection",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Whole-genome sequencing or MLST for outbreak tracing",
-      "16S rRNA sequencing not reliable alone (ECC highly similar)"
-    ]
+
+  "field_notes": {
+    "Lactose Fermentation": "Often delayed or variable on MacConkey Agar.",
+    "Motility": "Most species are motile, but non-motile strains occur.",
+    "Indole": "Indole reactions vary by species and are not genus-defining."
   },
-  "notes": "Most clinically important species belong to the Enterobacter cloacae complex, which includes E. cloacae, E. hormaechei, and E. asburiae.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Enterobacter cloacae complex epidemiology",
-    "Healthcare-associated multidrug-resistant Enterobacter research"
+
+  "key_differentiators": [
+    {
+      "field": "VP",
+      "expected": "Positive",
+      "distinguishes_from": ["Escherichia", "Shigella"],
+      "notes": "VP positivity helps separate Enterobacter from MR-positive Enterobacterales."
+    },
+    {
+      "field": "Citrate",
+      "expected": "Positive",
+      "distinguishes_from": ["Escherichia"],
+      "notes": "Citrate utilization supports Enterobacter over E. coli."
+    },
+    {
+      "field": "Motility",
+      "expected": "Positive",
+      "distinguishes_from": ["Klebsiella"],
+      "notes": "Motility differentiates Enterobacter from typically non-motile Klebsiella."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Klebsiella",
+      "reason": "Shared lactose fermentation and mucoid colony appearance can cause confusion."
+    },
+    {
+      "genus": "Citrobacter",
+      "reason": "Overlapping biochemical reactions including citrate positivity and sugar fermentation."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Non-motile isolate with strong capsule suggests Klebsiella.",
+    "Indole-positive with MR-positive profile suggests Escherichia or Citrobacter.",
+    "H2S production argues against Enterobacter."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Indole test",
+      "reason": "Useful for narrowing species-level identification."
+    },
+    {
+      "test": "Motility testing",
+      "reason": "Helps distinguish from Klebsiella."
+    },
+    {
+      "test": "Molecular identification or MALDI-TOF",
+      "reason": "Recommended due to biochemical overlap within Enterobacterales."
+    }
+  ],
+
+  "supported_species": [
+    "cloacae",
+    "asburiae",
+    "hormaechei",
+    "kobei",
+    "ludwigii"
   ]
-}
+}