Quick Answer
Medical mycology is a compact, testable NEET PG microbiology cluster — five fungal genera dominate almost every stem.
- Candida — C. albicans common, C. auris the MDR Indian ICU nightmare; echinocandins first-line for invasive; central-line removal essential.
- Aspergillus — septate hyphae at 45° acute-angle branching; ABPA (asthmatic), aspergilloma (Monod sign), invasive (halo → air crescent); voriconazole first-line.
- Cryptococcus — India-ink halo in CSF, cryptococcal antigen (CrAg); AIDS-defining meningitis; AMBITION-cm regimen — single-dose 10 mg/kg LAmB + flucytosine + fluconazole × 14 days.
- Mucormycosis — broad, non-septate, right-angle hyphae; DKA + iron overload + immunosuppression; India COVID-19 second-wave surge (>47,000 cases); surgery + LAmB + isavuconazole.
- Pneumocystis jirovecii (PCP) — HIV CD4 <200; bilateral perihilar ground-glass + hypoxia; BAL silver stain; TMP-SMX ± steroids if PaO2 <70.
- India — Candida auris outbreaks in tertiary ICUs; COVID mucormycosis lessons; MDR fungal disease is a hospital-safety priority.
Medical mycology used to be a niche microbiology topic. After India's COVID-19-associated mucormycosis outbreak in 2021, the rise of Candida auris in ICUs across metros, and the growing HIV/AIDS-associated fungal burden, NEET PG examiners have doubled down on this cluster. Expect at least three or four questions across the microbiology and medicine papers.
This NEETPGAI deep dive walks through the four opportunistic mycoses that carry the highest exam weight — Candida, Aspergillus, Cryptococcus and Mucorales — plus PCP, the AIDS-defining pneumonia. Pair this with the HIV/AIDS management guide for the underlying immunosuppression context.
Candidiasis — from thrush to Candida auris
Candida species are yeasts that form part of the normal flora. Disease occurs when host defence is disrupted (antibiotics, catheters, diabetes, immunosuppression).
Species and susceptibility
| Species | Notable features | Antifungal susceptibility |
|---|
| C. albicans | Germ tube positive; commonest overall | Fluconazole susceptible |
| C. glabrata | No germ tube; small; ICU / haematology | Fluconazole reduced susceptibility; echinocandin first-line |
| C. tropicalis | Neutropenia-associated | Fluconazole variable |
| C. parapsilosis | Central-venous-line associated; hand carriage | Fluconazole susceptible; echinocandin MICs higher |
| C. krusei | Intrinsically fluconazole resistant | Echinocandin or amphotericin |
| C. auris | Multidrug resistant; outbreaks in Indian ICUs; misidentified by biochemical panels | Echinocandin first — many resistant to fluconazole and amphotericin |
Clinical spectrum
- Mucocutaneous — oral thrush (curd-like plaques scraped off), angular cheilitis, oesophageal candidiasis (AIDS-defining if CD4 low), vulvovaginal candidiasis, diaper candidiasis, chronic mucocutaneous candidiasis in STAT1 gain-of-function.
- Invasive candidiasis — candidemia, disseminated candidiasis (endophthalmitis, hepatosplenic microabscesses, endocarditis on prosthetic valves).
- Nosocomial risk factors — central venous catheter, broad-spectrum antibiotics, TPN, abdominal surgery, ICU stay, neutropenia.
Diagnosis and treatment
- Blood cultures (BacT/Alert, lysis-centrifugation) — positive in 50–75% of candidemia only; low sensitivity.
- Beta-D-glucan (BDG) — pan-fungal marker (positive in Candida, Aspergillus, PCP; negative in Cryptococcus and mucormycosis).
- MALDI-TOF — species identification within minutes; critical for detecting C. auris.
- Mucocutaneous — topical nystatin, clotrimazole; oral fluconazole for oesophageal or extensive disease.
- Invasive candidiasis — start empirical echinocandin (caspofungin, micafungin, anidulafungin); step down to fluconazole if C. albicans confirmed and stable. Always remove central lines and dilate pupils for funduscopy.
Aspergillosis — three completely different diseases
Aspergillus fumigatus (commonest), A. flavus, A. niger — septate hyaline hyphae with dichotomous branching at 45°.
Allergic bronchopulmonary aspergillosis (ABPA)
Hypersensitivity reaction, not invasion. Occurs in asthmatics and cystic fibrosis patients.
- Rosenberg-Patterson criteria — asthma, immediate skin-test reactivity to Aspergillus, precipitating antibodies, serum IgE > 1000 IU/mL, blood eosinophilia, central bronchiectasis, pulmonary infiltrates.
- Chest imaging — central (upper-lobe) bronchiectasis, fleeting infiltrates, "finger-in-glove" mucous plugs.
- Treatment — oral corticosteroids (backbone) + itraconazole for prolonged remission.
Aspergilloma (fungus ball)
Saprophytic colonisation of a pre-existing cavity — old tuberculosis, sarcoidosis, bulla.
- Monod sign on CT — solid mass separated from cavity wall by a crescent of air; changes position on prone imaging.
- Presentation — recurrent haemoptysis (can be massive and fatal).
- Treatment — surgical resection for haemoptysis; bronchial artery embolisation as bridge; voriconazole for non-surgical candidates.
Invasive pulmonary aspergillosis (IPA)
Life-threatening angioinvasive disease of profoundly neutropenic hosts (AML induction, HSCT, prolonged steroids).
- CT — early halo sign (nodule with ground-glass surround from haemorrhage); later air-crescent sign as neutrophils recover.
- Diagnosis — serum and BAL galactomannan (Aspergillus-specific), BDG (pan-fungal), BAL PCR, tissue culture and histology (septate hyphae, 45° branching).
- Treatment — voriconazole IV first-line (monitor levels, hepatotoxicity, visual disturbances). Alternatives: isavuconazole (less QT), liposomal amphotericin B, posaconazole for prophylaxis in high-risk haematology.
Cryptococcosis — the AIDS-defining meningitis
Cryptococcus neoformans (worldwide, pigeon droppings) and C. gattii (tropical, eucalyptus trees, immunocompetent hosts). Encapsulated yeast — the polysaccharide capsule is the virulence factor and the target of the CrAg antigen test.
Clinical
- Meningoencephalitis — subacute headache, fever, altered mental status, cranial neuropathies; raised intracranial pressure is common and predicts mortality.
- Pulmonary cryptococcosis — nodules or infiltrates; may be asymptomatic.
- Cutaneous cryptococcosis — molluscum-like papules (marker of dissemination).
Diagnosis
- CSF India ink — clear halo around yeast cell (the capsule) — classic teaching finding but ~60% sensitivity.
- Cryptococcal antigen (CrAg) on CSF and serum — lateral flow assay; >90% sensitive and specific; the current standard.
- CSF — high opening pressure, lymphocytic pleocytosis, low glucose, high protein.
- Culture — Sabouraud agar; slower.
Treatment — the AMBITION-cm regimen
WHO 2022 first-line for HIV-associated cryptococcal meningitis:
- Induction (14 days) — single high-dose liposomal amphotericin B 10 mg/kg on day 1 + flucytosine 100 mg/kg/day for 14 days + fluconazole 1200 mg/day for 14 days.
- Consolidation (8 weeks) — fluconazole 800 mg/day.
- Secondary prophylaxis — fluconazole 200 mg/day until CD4 sustained above 200 for at least 6 months on ART.
- Delay ART for 4–6 weeks to avoid IRIS-related deaths.
- Serial lumbar punctures to control raised ICP (removes CSF to keep pressure below 20 cmH2O).
- CrAg screening at CD4 <100 — pre-emptive fluconazole if positive.
Mucormycosis — the "black fungus" outbreak
Order Mucorales — Rhizopus, Mucor, Rhizomucor, Lichtheimia, Cunninghamella. Broad, ribbon-like, non-septate (pauciseptate) hyphae with right-angle branching. Angioinvasive → thrombosis → tissue necrosis.
India — the COVID-19 second-wave surge
India registered more than 47,000 cases of COVID-associated mucormycosis (CAM) between April and June 2021. The convergence — uncontrolled diabetes and DKA, inappropriate corticosteroid dosing (dexamethasone above RECOVERY protocol or steroids in mild disease), COVID-19 endothelial damage, and possibly zinc supplementation and industrial oxygen humidification — produced the largest mucormycosis cluster in medical history. State governments declared it a notifiable disease.
Risk factors
- Diabetic ketoacidosis (classic host — acidic + iron-rich = germination-friendly).
- Iron overload (deferoxamine actually promotes it — the drug is a siderophore Mucor uses).
- Prolonged neutropenia, HSCT, solid-organ transplant.
- Prolonged corticosteroids.
- Trauma, burns.
Clinical forms
| Form | Features |
|---|
| Rhino-orbital-cerebral | Facial pain, black eschar on palate/nose, ophthalmoplegia, proptosis, cavernous sinus involvement, intracranial extension |
| Pulmonary | Nodules, cavitation, angioinvasion, reverse halo sign |
| Cutaneous | Necrotic ulcer after trauma or IV catheter |
| Gastrointestinal | Neonatal / malnourished; high mortality |
| Disseminated | Multiple organs; mortality above 90% |
Diagnosis and treatment
- Clinical suspicion is everything — imaging (CT sinus, MRI brain), tissue biopsy (broad non-septate hyphae, right-angle branching), fungal culture (often negative because hyphae are fragile).
- Treatment — urgent surgical debridement (repeated), IV liposomal amphotericin B 5–10 mg/kg/day first-line, isavuconazole or posaconazole for step-down or salvage. Correct hyperglycaemia and taper steroids aggressively.
Pneumocystis jirovecii pneumonia (PCP)
Formerly P. carinii — reclassified as a fungus. AIDS-defining illness at CD4 <200; also seen in transplant, chemotherapy, and prolonged steroids.
- Clinical — subacute dyspnoea, dry cough, low-grade fever; exertional desaturation is a red flag.
- CXR — bilateral perihilar interstitial infiltrates (ground-glass); may be normal early.
- HRCT — diffuse ground-glass opacities sparing the periphery.
- Diagnosis — induced sputum silver stain (Grocott-Gomori) or BAL — cyst forms; PCR is more sensitive. Serum LDH high; BDG elevated.
- Treatment — TMP-SMX 15–20 mg/kg/day of TMP component, divided every 6–8 hours, for 21 days. Alternatives — clindamycin + primaquine, atovaquone, IV pentamidine.
- Adjunctive corticosteroids — add prednisolone 40 mg BD × 5 days, then taper over 21 days, when PaO2 <70 mmHg on room air or A-a gradient >35 mmHg. Cuts mortality roughly in half.
- Primary prophylaxis — TMP-SMX single-strength daily when CD4 <200, oropharyngeal candidiasis, or AIDS-defining illness. Continue until CD4 >200 sustained for 3 months on ART.
Endemic mycoses (brief)
Rarely tested but occasionally show up in AIIMS-style stems.
| Organism | Habitat | Key feature |
|---|
| Histoplasma capsulatum | Bird / bat droppings — Ohio-Mississippi; India sporadic | Intracellular yeast in macrophages; can mimic TB |
| Blastomyces dermatitidis | River-valley soil (North America) | Broad-based budding yeast |
| Coccidioides immitis | Southwest US desert | Spherule with endospores |
| Paracoccidioides brasiliensis | Latin America | "Mariner's wheel" appearance |
| Sporothrix schenckii | Rose thorn; India occasional | Lymphocutaneous nodular lymphangitis (rose-gardener disease) |
NEET PG MCQ traps
- C. auris — echinocandin first-line; MALDI-TOF for ID; contact precautions.
- Germ-tube test — positive in C. albicans (and C. dubliniensis).
- Candidemia — remove central line, dilate pupil, echocardiogram if prolonged.
- BDG — positive in Candida, Aspergillus, PCP; NEGATIVE in Cryptococcus and mucormycosis.
- Aspergillus branching — septate, 45° acute angle.
- Mucor branching — non-septate (pauciseptate), 90° right angle.
- ABPA — asthma + IgE >1000 + central bronchiectasis; steroids + itraconazole.
- Aspergilloma Monod sign — moves with position change.
- Halo sign — early invasive pulmonary aspergillosis.
- Air-crescent sign — later IPA on neutrophil recovery.
- Voriconazole — first-line IPA; monitor levels, hepatotoxicity, visual disturbances.
- Cryptococcus India ink — halo (capsule); CrAg >90% sensitive and specific.
- AMBITION-cm — single 10 mg/kg LAmB + flucytosine + fluconazole 14 days.
- Delay ART 4–6 weeks after starting cryptococcal induction.
- CrAg screening at CD4 <100.
- Mucor triad — DKA + facial pain + black eschar → rhino-orbital-cerebral mucormycosis.
- Deferoxamine — increases mucormycosis risk (Mucor uses it as siderophore).
- PCP — HIV CD4 <200; TMP-SMX; add steroids if PaO2 <70.
- PCP prophylaxis — starts at CD4 <200; stops when CD4 >200 sustained 3 months on ART.
- Silver stain — Grocott-Gomori methenamine silver — the go-to stain for Pneumocystis cysts.
India context and recent policy
- Candida auris — first reported from Delhi in 2011; India remains one of the world's leading contributors to case series; ICMR issued national guidance in 2019 and updated it in 2022 for infection control (chlorhexidine skin decolonisation, hydrogen peroxide vapour or sodium hypochlorite terminal cleaning).
- COVID-associated mucormycosis — declared notifiable during the second wave; state governments organised free amphotericin B distribution; ICMR/AIIMS guidance emphasised steroid stewardship in COVID (no steroids in mild disease, dexamethasone 6 mg for hypoxia — not higher doses).
- AMBITION-cm rollout — India NACO updated cryptococcal-meningitis guidance in 2022 to the single-dose LAmB regimen based on the AMBITION-cm New England Journal of Medicine trial.
- CrAg screening — WHO recommends CrAg screening at CD4 <100 in HIV; roll-out under NACO is progressing.
- Fungal-disease burden — LIFE (Leading International Fungal Education) estimates India has millions of chronic pulmonary aspergillosis, recurrent vulvovaginal candidiasis, ABPA and PCP cases annually; systematic surveillance is still limited.
- Isavuconazole — approved in India post-COVID mucormycosis outbreak; oral bioavailability and lower QT signal make it a step-down option after LAmB induction.
Frequently asked questions
Why has Candida auris become such an important nosocomial pathogen in Indian ICUs?
Candida auris was first identified in India in 2011 and now accounts for a large proportion of candidemia cases in Indian tertiary-care ICUs. Three features drive its clinical impact — it is intrinsically resistant to fluconazole, frequently resistant to amphotericin B and increasingly to echinocandins; it persists on plastic surfaces, ventilator tubing and skin colonisation for weeks despite standard disinfection; and it is easily misidentified by conventional biochemical tests as C. haemulonii or Rhodotorula. Diagnosis needs MALDI-TOF or molecular methods. Empirical treatment for suspected C. auris candidemia is an echinocandin (caspofungin, micafungin, anidulafungin) with susceptibility-guided step-down. Central-line removal and strict contact precautions with chlorhexidine skin decolonisation are essential.
How do you distinguish invasive pulmonary aspergillosis from an aspergilloma on imaging?
Aspergilloma is a saprophytic fungus ball that colonises a pre-existing cavity (old TB, sarcoidosis, bulla). Chest CT shows a rounded intracavitary mass separated from the cavity wall by a crescent of air — the Monod sign — that moves with position change. It typically causes recurrent haemoptysis and does not invade tissue. Invasive pulmonary aspergillosis (IPA) occurs in profoundly neutropenic hosts (haematological malignancy, transplant). CT shows the halo sign early (nodule surrounded by ground-glass haemorrhage) and, as neutrophils recover, the air-crescent sign appears within the nodule. IPA is a medical emergency needing voriconazole or isavuconazole. ABPA is different again — a hypersensitivity reaction in asthmatics and cystic fibrosis with central bronchiectasis, high IgE and Aspergillus-specific IgE.
What is the standard induction regimen for cryptococcal meningitis in HIV in India?
The WHO 2022 and India NACO regimen for HIV-associated cryptococcal meningitis is induction with a single high dose of liposomal amphotericin B (10 mg per kg) plus flucytosine 100 mg per kg per day and fluconazole 1200 mg per day for 14 days — the AMBITION-cm trial regimen, which cut 10-week mortality and is now first-line. Consolidation is fluconazole 800 mg per day for 8 weeks, followed by secondary prophylaxis fluconazole 200 mg per day until CD4 is above 200 sustained on ART for 6 months. ART is delayed by 4 to 6 weeks to reduce IRIS-related deaths. Serial lumbar punctures manage raised intracranial pressure, and cryptococcal antigen screening at CD4 under 100 identifies patients for pre-emptive fluconazole.
Why did India see such a large mucormycosis outbreak during the COVID-19 second wave?
India recorded more than 47,000 cases of COVID-associated mucormycosis during the April to June 2021 second wave — the largest cluster in medical history. Three risk factors converged: (1) uncontrolled diabetes and diabetic ketoacidosis, which provide the acidic iron-rich environment Mucorales need for germination; (2) inappropriate corticosteroid dosing (dexamethasone doses exceeding the RECOVERY protocol, or steroid use in mild disease); and (3) COVID-19 itself with its endothelial damage, hyperglycaemia and immune dysregulation. Rhino-orbital-cerebral mucormycosis presented with facial pain, black eschar of the palate or nose, ophthalmoplegia and rapid intracranial extension. Treatment is aggressive surgical debridement plus IV liposomal amphotericin B, correcting hyperglycaemia and tapering steroids. Isavuconazole and posaconazole are step-down or salvage options.
When is prophylactic TMP-SMX indicated in HIV and how does it treat established PCP?
Trimethoprim-sulfamethoxazole (TMP-SMX or co-trimoxazole) is the drug of choice for both Pneumocystis jirovecii pneumonia (PCP) treatment and prevention. Primary prophylaxis is started when CD4 falls below 200 cells per microlitre or the patient has oropharyngeal candidiasis, an AIDS-defining illness, or CD4 percentage under 14. It also covers cerebral toxoplasmosis when CD4 is under 100 and Toxoplasma serology is positive. Treatment dose is 15 to 20 mg per kg per day of the trimethoprim component, divided every 6 to 8 hours for 21 days. If room-air PaO2 is under 70 mmHg or the A-a gradient exceeds 35 mmHg, add prednisolone starting at 40 mg twice daily for 5 days, tapering over 21 days — this cuts respiratory failure and mortality by roughly half. Prophylaxis continues until CD4 is above 200 for at least 3 months on suppressive ART.
This content is for educational purposes for NEET PG exam preparation. It is not a substitute for professional medical advice, diagnosis, or treatment. Clinical information has been reviewed by qualified medical professionals.
Written by: NEETPGAI Editorial Team
Reviewed by: Pending SME Review
Last reviewed: July 2026
