Update data/rag/knowledge_base/Clostridioides/difficile.json

data/rag/knowledge_base/Clostridioides/difficile.json

@@ -1,56 +1,124 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Clostridioides",
   "species": "difficile",
-  "full_name": "Clostridioides difficile",
-  "clinical_significance": "The causative agent of C. difficile infection (CDI), including antibiotic-associated diarrhea, pseudomembranous colitis, fulminant colitis, and toxic megacolon. Major healthcare-associated pathogen with significant morbidity and mortality. Spread enhanced by highly resistant environmental spores.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive rods with subterminal spores; may appear Gram-variable after 24 hours.",
-    "culture": "Yellowish, ground-glass colonies with horse-stable odor. Fluoresces chartreuse under UV. Grows on CCFA/CHROMID C. difficile media.",
-    "biochemical": [
-      "Strict anaerobe",
-      "Catalase negative",
-      "Indole negative",
-      "Motile (flagellated)",
-      "No growth in 6.5% NaCl",
-      "Ferments amino acids and produces p-cresol"
-    ]
+
+  "overview": {
+    "short": "Clostridioides difficile is a Gram-positive, anaerobic, spore-forming rod and a leading cause of antibiotic-associated diarrhoea and pseudomembranous colitis.",
+    "clinical_context": "Classically associated with recent antibiotic exposure, healthcare settings, and detection of toxin production."
   },
-  "differentiation": {
-    "from close species": [
-      "Toxin genes tcdA and tcdB define pathogenic strains.",
-      "Binary toxin (CDT) in hypervirulent strains (e.g., ribotype 027).",
-      "Fluorescent colonies under UV differentiate from many anaerobes.",
-      "Has a distinctive odor unlike C. mangenotii."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "CCFA Agar"
     ],
-    "from other genera": [
-      "Bacteroides are Gram-negative and non-spore-forming.",
-      "Clostridium perfringens is lecithinase positive and grows more rapidly.",
-      "Peptoclostridium difficile (old name) is no longer taxonomically valid."
-    ]
+    "Colony Morphology": [
+      "Irregular",
+      "Flat",
+      "Grey"
+    ],
+    "Oxygen Requirement": "Anaerobic",
+    "Growth Temperature": "25//42",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Variable"
   },
-  "virulence_factors": [
-    "Toxin A (TcdA): enterotoxin causing fluid secretion",
-    "Toxin B (TcdB): cytotoxin causing cell rounding and death",
-    "Binary toxin (CDT) in hypervirulent strains",
-    "Spore formation enabling environmental persistence",
-    "Adhesins enabling colonization during antibiotic disruption"
+
+  "species_markers": [
+    {
+      "field": "Motility",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Motility supports C. difficile in context, but is not exclusive among anaerobic rods."
+    },
+    {
+      "field": "Indole",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Indole negativity helps distinguish from certain other clostridial anaerobes."
+    },
+    {
+      "field": "Media Grown On",
+      "value": "CCFA Agar",
+      "importance": "high",
+      "notes": "Growth on selective media supports isolation/confirmation in appropriate clinical context."
+    }
   ],
-  "confirmation_methods": [
-    "PCR for tcdA/tcdB genes",
-    "GDH antigen + toxin EIA algorithm",
-    "Tissue culture cytotoxicity assay",
-    "MALDI-TOF MS for organism ID"
+
+  "common_confusions": [
+    {
+      "species": "Clostridioides mangenotii",
+      "reason": "Same genus and broad anaerobic spore-forming profile; requires higher-resolution confirmation."
+    },
+    {
+      "genus": "Clostridium",
+      "reason": "Many species are anaerobic spore-forming rods with overlapping biochemical reactions."
+    }
   ],
-  "treatment_notes": [
-    "First-line: oral vancomycin or fidaxomicin",
-    "Metronidazole only for mild disease or when other agents unavailable",
-    "Fecal microbiota transplantation (FMT) for recurrent CDI",
-    "Bezlotoxumab adjunct for recurrence reduction"
+
+  "when_to_question_identification": [
+    "Lack of anaerobic growth suggests an aerobe/facultative organism rather than Clostridioides.",
+    "Non-spore-forming phenotype argues strongly against C. difficile.",
+    "If clinical context is not gastrointestinal/antibiotic-associated, consider alternative anaerobes."
   ],
-  "notes": "Hypervirulent strains (e.g., BI/NAP1/027) have increased toxin production, higher recurrence, and increased severity.",
-  "references": [
-    "IDSA/SHEA CDI treatment guidelines",
-    "C. difficile pathogenesis literature",
-    "Epidemiology of hypervirulent strains"
+
+  "recommended_next_tests": [
+    {
+      "test": "Toxin A/B detection (EIA) or GDH + toxin algorithm",
+      "reason": "Toxin detection is central to clinically relevant identification of toxigenic C. difficile.",
+      "api_kit_example": "C. difficile GDH + toxin A/B rapid immunoassay kits (varies by lab supplier)."
+    },
+    {
+      "test": "NAAT (PCR) for toxin genes (e.g., tcdB)",
+      "reason": "High sensitivity confirmation for toxigenic strains when algorithm indicates.",
+      "api_kit_example": "C. difficile toxin gene NAAT/PCR assay kits (platform-dependent)."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable organism identification; toxin status still requires toxin/NAAT testing."
+    }
   ]
-}
+}