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{
"schema_version": "1.0",
"level": "species",
"genus": "Clostridioides",
"species": "difficile",
"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."
},
"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"
],
"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"
},
"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."
}
],
"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."
}
],
"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."
],
"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."
}
]
} |