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

data/rag/knowledge_base/Enterobacter/hormaechei.json

@@ -1,54 +1,126 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Enterobacter",
   "species": "hormaechei",
-  "full_name": "Enterobacter hormaechei",
-  "clinical_significance": "The most clinically relevant member of the Enterobacter cloacae complex, frequently implicated in multidrug-resistant hospital outbreaks. Major cause of nosocomial pneumonia, bacteremia, neonatal sepsis, and device-related infections. High propensity for AmpC overexpression, ESBL production, and carbapenemase acquisition (KPC, NDM, OXA-48).",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Lactose fermenting colonies; identical appearance to other ECC species.",
-    "biochemical": [
-      "Indole negative",
-      "Citrate positive",
-      "ONPG positive",
-      "Lysine decarboxylase positive",
-      "Ornithine decarboxylase positive",
-      "Gas from glucose variable",
-      "Urease negative or weak",
-      "Motile"
-    ]
+
+  "overview": {
+    "short": "Enterobacter hormaechei is a Gram-negative, facultatively anaerobic rod and a major member of the Enterobacter cloacae complex, frequently implicated in nosocomial infections.",
+    "clinical_context": "Commonly isolated from bloodstream, respiratory, urinary, and device-associated infections, particularly in healthcare settings."
   },
-  "differentiation": {
-    "from close species": [
-      "Most outbreak-prone ECC member.",
-      "More frequently associated with carbapenemase genes than E. cloacae or E. asburiae.",
-      "Indole negative similar to E. cloacae—requires MALDI-TOF or WGS for species-level ID."
+
+  "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": [
-      "Motility differentiates from Klebsiella.",
-      "Lysine positive vs Citrobacter.",
-      "DNase negative vs Serratia."
-    ]
+    "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": "Variable",
+    "Esculin Hydrolysis": "Positive",
+    "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": "Variable",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Positive",
+    "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": [
-      "Inducible and derepressed AmpC",
-      "Carbapenemases (KPC, NDM, VIM, OXA-48–like variants)",
-      "Biofilm formation on medical devices",
-      "Efflux pumps and porin mutations"
+
+  "species_markers": [
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key discriminator separating E. hormaechei from other members of the E. cloacae complex."
+    },
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Helps distinguish E. hormaechei from E. cloacae, which is typically rhamnose negative."
+    },
+    {
+      "field": "Gelatin Hydrolysis",
+      "value": "Variable",
+      "importance": "medium",
+      "notes": "Less reliable alone but supportive when combined with other markers."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS (best practical approach)",
-      "Whole-genome sequencing for outbreak investigation",
-      "Carbapenemase PCR when resistant"
+
+  "common_confusions": [
+    {
+      "species": "Enterobacter cloacae",
+      "reason": "Very close biochemical overlap within the Enterobacter cloacae complex."
+    },
+    {
+      "species": "Enterobacter asburiae",
+      "reason": "Shared sugar fermentation patterns and citrate positivity."
+    }
   ],
-  "treatment_notes": [
-      "Cefepime preferred over 3rd-gen cephalosporins.",
-      "If CRE: ceftazidime–avibactam, meropenem–vaborbactam, or novel β-lactam/β-lactamase inhibitors.",
-      "Piperacillin–tazobactam variable; avoid monotherapy in severe disease."
+
+  "when_to_question_identification": [
+    "Ornithine decarboxylase negativity suggests E. cloacae rather than E. hormaechei.",
+    "Rhamnose negativity is inconsistent with E. hormaechei.",
+    "Indole positivity suggests a different Enterobacter species."
   ],
-  "notes": "Species is subdivided into several subspecies (e.g., E. hormaechei subsp. steigerwaltii, subsp. xiangfangensis) that dominate global hospital outbreaks.",
-  "references": [
-      "Enterobacter hormaechei outbreak genomics",
-      "CRE surveillance data",
-      "AmpC derepression studies"
+
+  "recommended_next_tests": [
+    {
+      "test": "Ornithine decarboxylase",
+      "reason": "Primary biochemical discriminator within the E. cloacae complex."
+    },
+    {
+      "test": "Rhamnose fermentation",
+      "reason": "Useful supporting discriminator when ornithine is positive."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred method for accurate species-level identification within the complex."
+    },
+    {
+      "test": "Whole genome sequencing",
+      "reason": "Definitive identification when clinically significant or outbreak-related."
+    }
   ]
-}
+}