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

data/rag/knowledge_base/Enterobacter/cloacae.json

@@ -1,53 +1,122 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Enterobacter",
   "species": "cloacae",
-  "full_name": "Enterobacter cloacae",
-  "clinical_significance": "A major member of the Enterobacter cloacae complex (ECC) and one of the most common nosocomial pathogens. Causes UTIs, pneumonia (especially ventilator-associated), bacteremia, intra-abdominal infections, and device-related infections. AmpC hyperproduction and ESBL or carbapenemase acquisition are common.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Lactose fermenting or late lactose fermenting colonies on MacConkey.",
-    "biochemical": [
-      "Indole negative (typical)",
-      "Citrate positive",
-      "ONPG positive",
-      "Lysine decarboxylase positive",
-      "Ornithine decarboxylase positive",
-      "Gas from glucose variable",
-      "Urease negative or weak",
-      "Motile"
-    ]
+
+  "overview": {
+    "short": "Enterobacter cloacae is a Gram-negative, facultatively anaerobic rod commonly associated with opportunistic and nosocomial infections.",
+    "clinical_context": "Frequently isolated from urinary tract, respiratory, and bloodstream infections, particularly in hospital settings."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole negative differentiates it from some E. asburiae strains.",
-      "Often hyperproduces AmpC β-lactamase, leading to resistance during therapy.",
-      "Difficult to distinguish biochemically from E. hormaechei; MALDI-TOF or WGS required."
+
+  "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": [
-      "Motile vs Klebsiella (non-motile).",
-      "Lysine positive vs Citrobacter (lysine negative).",
-      "DNase negative vs Serratia (DNase positive)."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "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": "Positive",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "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": "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": [
-      "Inducible AmpC β-lactamase",
-      "Biofilm formation",
-      "Permeability mutations increasing carbapenem resistance",
-      "LPS-mediated inflammation"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Helps distinguish E. cloacae from indole-positive Enterobacter species."
+    },
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Useful discriminator within the Enterobacter cloacae complex."
+    },
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Supports identification when combined with other biochemical results."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Whole-genome sequencing for ECC resolution",
-      "AmpC detection assays"
+
+  "common_confusions": [
+    {
+      "species": "Enterobacter hormaechei",
+      "reason": "Closely related species within the E. cloacae complex with overlapping biochemical profiles."
+    },
+    {
+      "genus": "Citrobacter",
+      "reason": "Shared citrate positivity and sugar fermentation patterns."
+    }
   ],
-  "treatment_notes": [
-      "Avoid 3rd-generation cephalosporins due to risk of AmpC induction.",
-      "Prefer carbapenems, cefepime, or piperacillin–tazobactam depending on MICs.",
-      "CRE strains require advanced agents (e.g., ceftazidime–avibactam)."
+
+  "when_to_question_identification": [
+    "Indole positivity suggests another Enterobacter species.",
+    "Strong lactose fermentation may indicate Klebsiella or Escherichia.",
+    "H2S production is inconsistent with E. cloacae."
   ],
-  "notes": "Part of a complex of >6 genospecies; misidentification common without molecular methods.",
-  "references": [
-      "ECC resistance mechanism literature",
-      "Hospital outbreak investigations involving Enterobacter"
+
+  "recommended_next_tests": [
+    {
+      "test": "Ornithine decarboxylase",
+      "reason": "Key discriminator within the Enterobacter cloacae complex."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable differentiation within the Enterobacter cloacae complex."
+    },
+    {
+      "test": "Molecular identification",
+      "reason": "Recommended due to close genetic similarity between species."
+    }
   ]
-}
+}