This case report describes a 42-year-old male farmer from Uttar Pradesh, India who presented with a 6-month history of cough and breathlessness. CT scans showed a mass lesion in his right upper, middle, and lower lobes. A biopsy was suggestive of fungal granuloma. The patient was treated with fluconazole for 4 months without improvement. Further workup including KOH preparation and Gram stain of a repeat biopsy showed features suggestive of Cryptococcus species, though cultures were negative. This case suggests a possible fungal infection such as cryptococcosis as the underlying etiology.

1. Immunodeficiency
Disorders- Tutorials
Presenter- Dr. Bishal Gupta
Moderator- Dr. Chinmoy Sahu
Date- 27.01.2023

2. Introduction
• Immunodeficiency - state where the defence mechanisms of the body are impaired,
leading to enhanced susceptibility to microbial infections as well as to certain forms of
cancer
• Immunodeficiency diseases are broadly classified as:
Primary immunodeficiency
Secondary immunodeficiency

4. Humoral immunodeficiency (B cell defects)
 Bruton disease (X-linked
agammaglobulinemia)
 Common variable immunodeficiency
 Isolated IgA deficiency
 Hyper-IgM syndrome
Cellular immunodeficiencies (T cell defects)
 DiGeorge syndrome (thymic hypoplasia)
 Chronic mucocutaneous candidiasis
 Purine nucleoside phosphorylase (PNP)
deficiency
Disorders of complement
 Complement component deficiencies
 Complement regulatory protein deficiencies
Combined immunodeficiencies (B and T cell
defects)
 Severe combined immunodeficiencies
• Cytokine receptor mutation
• Adenosine deaminase (ADA) deficiency
 Wiskott–Aldrich syndrome
 Ataxia telangiectasia
 Nezelof syndrome
Disorders of phagocytosis
 Chronic granulomatous disease
 Myeloperoxidase deficiency
 Chediak–Higashi syndrome
 Leukocyte adhesion deficiency
 Lazy leukocyte syndrome
 Job’s syndrome or Hyper-IgE syndrome

5. Bruton Disease (X-linked
Agammaglobulinemia)
• Failure of pre-B cells to differentiate into immature B cells in the bone marrow
• Due to absence of an enzyme called Bruton’s tyrosine kinase (transformation of pre-B cell
into immature B cell)  Total absence of B cells and plasma cells in the circulation
• Pre-B cells are found in normal numbers in bone marrow and the T-cell-mediated
responses are also normal
• Cytoplasm of pre B cell may have incomplete immunoglobulins
• X linked, primarily in males; nevertheless, sporadic cases have been described in females

6. • Secondary infections are seen after 6 months of age, when maternal antibodies are
depleted
Recurrent bacterial infections (e.g., Haemophilus influenzae, Streptococcus
pneumoniae, or Staphylococcus aureus) leading to acute and chronic pharyngitis,
sinusitis, otitis media, bronchitis, and pneumonia
Viruses that are cleared by neutralizing antibodies- e.g. enteroviruses
Parasites which are usually resisted by secretory IgA- e.g. Giardia lamblia

7. Common Variable Immunodeficiency
• Heterogeneous group of both sporadic and inherited forms of the disease
• Hypogammaglobulinemia, increased susceptibility to infection, autoimmune disorders
(hemolytic anemia, pernicious anemia), as well as lymphoid tumors
• Clinical manifestations are superficially similar to those of Bruton diseases; but differ in
the following aspects:
Both sexes are affected equally
Onset of symptoms is much later - second or third decade of life
B cell development defect
Intrinsic B-cell defects, deficient T-cell help, or excessive T-cell suppressor activity

8. Isolated IgA Deficiency
• Most common, affects about 1 in 700 white individuals
• Weakened mucosal defences due to IgA deficiency predispose patients to recurrent
sinopulmonary infections and diarrhea
• Significant (but unexplained) association with autoimmune diseases
• Pathogenesis:
 Block in the terminal differentiation of IgA-secreting B cells to plasma cells (due to altered T-
cell production of cytokines or intrinsic B-cell defect)
The levels of other immunoglobulins are usually normal or even excess

9. Hyper-IgM Syndrome
• X-linked disorder - due to a defect in isotype class switchover of B cells
• Mutations in either CD40L or CD40 genes, leading to prevention of interaction between T and B-cell ; thus
blocking the class switchover
• Block in class switchover results in lack of synthesis of other classes of antibodies - IgG, IgA, and IgE with a
normal or supernormal levels of IgM
• Deficiency of IgG – leads to defect in opsonization and complement activation (predisposes to recurrent
pyogenic infections)

10. Hyper-IgM Syndrome
• IgA deficiency leads to increased recurrent sinopulmonary infections
and diarrhea
• Excess IgM antibodies can react with blood cells, resulting in
autoimmune hemolytic anemia, thrombocytopenia, or neutropenia
• Patients with defect in CD40L are more susceptible to Pneumocystis
jirovecii infection

11. DiGeorge Syndrome (Thymic Aplasia)
• Results from a congenital defect in thymic development leading to defect in T-cell
maturation
• Infants are extremely vulnerable to viral, fungal, intracellular bacterial and protozoan
infections
• Pathogenesis- In 90% of cases, there occurs a deletion affecting chromosome 22q11
which leads to developmental malformation affecting the third and fourth pharyngeal
pouches in embryonic life
• Thymus, parathyroid glands, and portions of the face and aortic arch become defective

12. DiGeorge Syndrome (Thymic Aplasia)
• There may be associated:
Parathyroid gland hypoplasia resulting in neonatal tetany and hypocalcemia
Anomalies of the heart and the great vessels (Fallot's Tetralogy)
Characteristic facial appearance
• Treatment- Thymus transplantation has been found to be successful in restoration of
immune function. In others (with partial defects), immunity may improve spontaneously
with age

13. • CATCH 22

14. Chronic Mucocutaneous Candidiasis
• Represents an impaired cell-mediated immunity against Candida albicans
leads to superficial infections of the skin, mucous membranes, and nails
• Do not show increased susceptibility to other infections but often
associated with endocrinopathies and autoimmune disorders (vitiligo,
malabsorption syndromes)
• Transfer factor therapy, along with fluconazole has been reported to be
effective

15. Severe Combined Immunodeficiencies
(SCID)
• Represents groups of genetically distinct syndromes; all having in common,
defects in both humoral and cell-mediated immune responses
• Severe: implies complete absence of T cell function, death in first year
• Mutation in cytokine receptor - Approximately 50-60% of the cases of SCID
are X-linked (seen in males)
• Results from mutations in the gene encoding the common γ chain shared
by the cytokine receptors for IL-7 and others (IL-2, IL-4, IL-9, and IL-15)
• Defective IL-7 receptor - defect in survival and expansion of immature B-
and T-cell precursors in the bone marrow
• Defect in IL-15 receptor - deficiency of NK cell

16. Types of SCID
• Adenosine deaminase (ADA) deficiency - Most common, ADA deficiency leads to accumulation of
deoxyadenosine which is toxic to rapidly dividing immature T lymphocytes
• RAG Mutation- Recombinase-activating genes (RAG) defect blocks the development of T and B
cells
• Jak3 mutation- Jak3, an intracellular kinase mutation is another way of blocking the cytokine
receptor signalling
• Class II MHC deficiency-Mutations that impair the expression of class II MHC molecules prevent
the development of CD4+ T cells. This condition is also called the bare lymphocyte syndrome

17. SCID
• Affected infants are susceptible to
severe recurrent infections by a wide
array of pathogens, including Candida,
Pneumocystis, cytomegalovirus, and
Pseudomonas
• Bone marrow transplantation. Gene
therapy replacing the mutated genes
has been successful in X linked cases

18. Wiskott–Aldrich Syndrome (WAS)
• X-linked recessive disease
• Characterized by immunodeficiency with thrombocytopenia, eczema(triad)
• Severity of WAS increases with age
• First manifests itself by defective responses to bacterial polysaccharides and by lower IgM levels.
IgG levels are usually normal
Paradoxically the levels of IgA and IgE are often elevated
• Other T and B cell responses are normal initially, but with increase of age, there are recurrent
bacterial infections and a gradual loss of humoral and cellular responses
• Prone to develop non-Hodgkin B-cell lymphomas
• Bloody diarrhea secondary to thrombocytopenia

19. Wiskott–Aldrich Syndrome (WAS)
• Pathogenesis:
Genetic defect is due to a mutation in the gene encoding Wiskott-Aldrich syndrome
protein (WASP) present in precursor lymphoid cells of bone marrow
Cytoskeletal glycoprotein (sialophorin or CD43), required for actin polymerization

20. Ataxia Telangiectasia
• Difficulty in maintaining balance while walking (cerebellar ataxia)
• Appearance of broken capillaries (telangiectasia) in the eyes and
choreoathetoid movements (usually noticed in infancy)
• Deficiency of IgA and sometimes IgE
• Profound sinopulmonary infections
• Primary defect - kinase involved in regulation of the cell cycle

21. Nezelof Syndrome
• Autosomal recessive
• Cellular immunodeficiency resulting from thymus hypoplasia
• In some patients, B cells are normal, whereas in others a B-cell
deficiency is secondary to the T-cell defect
• Affected individuals suffer from chronic diarrhea, viral and fungal
infections, and a general failure to thrive

22. Chronic Granulomatous Disease (CGD)
• Pathogenesis:
Involves inherited defects in the gene encoding components of oxidase
system
E.g. Nicotinamide adenine dinucleotide phosphate (NADP) oxidase of
phagocyte which breaks down hydrogen peroxide to generate free oxygen
radicals (O2
-) that are involved in microbial killing
Decreased oxidative burst which predisposes to recurrent bacterial infections.
CGD is a genetic disease that runs in family in two forms
• X linked form (more common, 70%) - membrane component of phagocyte
oxidase is defective
• Autosomal recessive form- cytoplasmic component of phagocyte oxidase is
defective

23. Chronic Granulomatous Disease (CGD)
• Manifestations-
Bacteria involved in the recurrent infections are catalase positive; pyogenic
pathogens such as staphylococci, Pseudomonas and coliforms
Excessive inflammatory reactions that result in gingivitis, swollen lymph nodes, and
non-malignant granulomas (lumpy subcutaneous cell masses)
Nitroblue tetrazolium reduction test (NBT) is used for screening to detect deficiency
of NADPH oxidase activity

24. Myeloperoxidase Deficiency
• Common genetic disorder characterized by deficiency in either
quantity or function, of myeloperoxidase, an enzyme produced by
neutrophils
• Patients present with immune deficiency and recurrent infections,
especially with Candida albicans

25. Chediak–Higashi Syndrome
• Autosomal recessive disease
• Defective fusion of phagosomes and lysosomes in phagocytes which leads to
increased susceptibility to recurrent and severe pyogenic infections
• Abnormalities in melanocytes leading to albinism (lack of skin and eye pigment)
• Abnormalities in cells of the nervous system (associated with nerve defects), and
• Platelets abnormalities, causing bleeding disorders
• Aggressive but non-malignant infiltration of organs by lymphoid cells

26. Chediak–Higashi Syndrome
• Pathogenesis:
Mutation in a protein called LYST (regulate lysosomal trafficking)
 Impairs the targeting of proteins to secretory lysosomes, which makes them unable
to lyse bacteria
 Phagocytes from patients with this immune defect contain giant granules but do not
have the ability to kill bacteria

27. Leukocyte Adhesion Deficiency (LAD)
• Rare autosomal recessive disorder, characterized by a defect in the
adhesion of leukocytes which results in poor leukocyte chemotaxis
particularly of neutrophils
• Predisposes to various bacterial and fungal infections
• Due to mutations in β2 integrin subunit (CD18) of the leukocyte cell
adhesion molecule or fucosyltransferase enzyme

28. Lazy Leukocyte Syndrome
• Idiopathic condition due to defect in neutrophil chemotaxis
• Increased pyogenic infections such as gingivitis, abscess formation,
pneumonia and neutropenia

29. Job’s Syndrome (Hyper-IgE Syndrome)
• Hyper-IgE syndrome - rare primary immunodeficiency disease
characterized by eczema, recurrent staphylococcal skin abscesses,
recurrent lung infections (pneumatocele), eosinophilia and high
serum levels of IgE
• Underlying mechanism - defect in neutrophil chemotaxis; due to
mutations in STAT3 or DOCK8 genes

30. SECONDARY IMMUNODEFICIENCIES
• Secondary effects of other diseases such as-
Malnutrition (due to inadequate immunoglobulin synthesis)
Aging (suppression of immune system with age)
Patients with several infections that supresses immune system causing lymphocyte
depletion, e.g. HIV (human immunodeficiency virus) infection.
Underlying cancers (particularly those of the bone marrow and blood cells (leukemia,
lymphoma, multiple myeloma)
Underlying proteinuric renal diseases– leads to loss of immunoglobulins
Sarcoidosis
Patients on immunosuppressive medications
Patients receiving chemotherapy or radiation therapy for malignancy

33. Pathogen Type T-Cell Defect B-Cell Defect Granulocyte
Defect
Complement
Defect
Bacteria Bacterial sepsis Streptococci,
Staphylococci,
Haemophilus
influenzae
Staphylococci,
Pseudomonas
Nocardia
Neisseria,
Other pyogenic
infections
Viruses Cytomegalovirus,
Epstein-Barr virus,
Severe varicella,
Chronic infections
with respiratory
and intestinal
viruses
Enterovirus
encephalitis
-
Fungi Candida,
Pneumocystis
- Candida,
Aspergillus

34. Pathogen Type T-Cell Defect B-Cell Defect Granulocyte Defect Complement Defect
Parasites - Giardiasis -
Special features Aggressive disease
with opportunistic
pathogens, failure to
clear infections
Recurrent
sinopulmonary
infections,
Sepsis, chronic
meningitis
-

35. Case1
• 42 / male from Balrampur, Uttar Pradesh was cough and breathlessness since 6 months
• He had a history of taking anti tubercular therapy 15 years ago but there was no documentation
• He had no history of COVID-19 illness
• There was no history of diabetes,hypertension, ischaemic heart disease
• Patient was smoker for 20 years,quit smoking 5 years ago
• He is farmer by occupation
• CT guided biopsy of the mass lesion (done on 1/7/22) was done outside and was suggestive of
fungal granuloma , while work up for TB was negative
• Patent was initiated on empirical anti-fungals (Fluconazole 400mg/day); which he has taken for 4
months- however there is no clinic-radiological improvement. He was thus referred to Dept. of
Pulmonary Medicine at our hospital

36. Figure showing CT Thorax- homogenous soft tissue
lesion in the right upper lobe, right middle lobe, and
superior segment of RLL with non enhancing
necrotic component
Figure showing Chest Xray with lobulated
spiculated mass covering upper and middle lobe

37. Work up
• Repeat CT guided biopsy was done and the biopsy sample was sent to microbiology department for further
confirmation
• Mycobacterium tuberculosis complex was not detected by GeneXpert Assay. ZN stain was negative for acid
fast bacilli. Culture for tuberculosis was also negative
• 10% KOH wet shows plenty of tissue debris and plenty capsulated round budding yeast suggestive of
Cryptococcus spp
• Grams’s stain also showed 5-10 micrometer round double walled spherical structures with gram positive
stippling suggestive of Cryptococcus spp
• However culture was negative after 6 weeks of incubation

38. Figure showing 10% KOH preparation of
lung tissue round yeast cells(yellow arrow)
Figure showing Gram’s stain- 5-10 micrometer round
double walled spherical structures with gram positive
stippling (yellow arrow)

39. Figure showing cryptococcal antigen from lung tissue sample
with titre 1:8

40. Further Work up
• HIV 1 and 2- Not detected
• HbsAg- Not detected
• Anti HCV-Not detected
• Serum IgA-324 mg/dl (Normal range 90-450 mg/dl)
• Serum IgE- 1799 iu/ml
• Serum IgM- 82.3 mg/dl (Normal range 60-280 mg/dl)
• Serum IgG= 1630 mg/dl (Normal range 800-1800 mg/dl)

42. • His absolute CD4 count was 173 per cmm. Suggestive of CD4
lymphopenia
• Final Diagnosis- Lung mass caused by Cryptococcus spp in a patient
of isolated CD4 lymphopenia.

43. • Total Duration of Illness – 2 years
• Dec 2020: Fever, cough for 1 week
• Jan 2021: Fever, cough, shoertness of breath treated
as pneumonia with IV antibiotic for 1 month(Needed
hospital admission)
• Oct 2021: Fever, cough – admitted and treated 1 week
• Dec 2021: Petechial rash over bilateral hands, chest,
abdomen, no h/o mucosal lesions, reduced platelet. No
platelet transfusion was given. Symptoms resolved in 4
days
• April 2022: Fever, with raised TLC around 24000,
Treated for 2 days. Hb 7. Platelet – 33k. 1 PRBC was
transfused
• June 2022: 3 platelets transfused. BMA – Congenital
amegakaryocytic thrombocytopenia
• Aug-Sept 2022: On oral folate,
• Oct 2022: Thrombocytopenia, PLT – 33k. TLC 50,000.
TLC 26000, L 88, N8
• Two of his sibling died

44. Further Work up
• HIV 1 and 2- Not detected
• HbsAg- Not detected
• Anti HCV-Not detected
• Serum IgA-6.67 mg/dl (Normal range 90-450 mg/dl)
• Serum IgE- 5 iu/ml
• Serum IgM- 4.17 mg/dl (Normal range 60-280 mg/dl)
• Serum IgG= 33.3 mg/dl (Normal range 800-1800 mg/dl)

45. • Total lymphocytes: 68%,
• T cell- 97%, B cell - 0.01%, NK cell - 2%,
• Of the CD3+ T Cells:- CD4 positive T cells: 3%, CD8 Pos T Cells:
86%, DNTs- 11%.
CD4:CD8 ratio is 1:29

47. Case 3
• 27/ M from a site manager of fertilizer unit
• TDI – 2 yrs
• Aug 2020: Weight loss 1 yr – 13 kg, fever low grade 3 months, night
sweats, abdominal pain
• Started on emperical ATT (outside)
• ill defines hypodense lesions in spleen, minimal ascites,
retroperitoneal lymphadenopathy
• Patient started feeling well on ATT , fever resolved, there was weight
gain
• July 2021: Completed ATT for 1 yr

48. Present illness
• Nov 2022: 1 month history of cough with expectoration, myalgia,
fever low grade with loose stool for for 15 days
• CT thorax – multilobar bronchial wall thickening and mild dilatation
with clusters of branching centrilobular nodules in bilateral lower
lobes
• Multiple mediastinal, para tracheal and mesenteric nodes present

49. Course in SGPGIMS
• Admitted in SGPGIMS as a case of pneumonia
• He had leukopenia of 1900, ANC – 900
• Emperically started on cefoperazone- sulbactum and Teicoplanin
• He was afebrile after 3 days
• His sputum revealed Pseudomonas aeruninosa
• Gene Xpert sputum negative
• His lungs were clear. No active sputum or fever
• Hence Bone marrow analysis was done – BMA & Biopsy normal
• Stool examination- Giardia sp

50. Lymphocyte subset analysis
• low B cell count, normal NK, CD4, CD8, total T cell count

51. Further Work up
• HIV 1 and 2- Not detected
• HbsAg- Not detected
• Anti HCV-Not detected
• Serum IgA-6.67 mg/dl (Normal range 90-450 mg/dl)
• Serum IgE- 5 iu/ml
• Serum IgM- 8.08 mg/dl (Normal range 60-280 mg/dl)
• Serum IgG= 33.3 mg/dl (Normal range 800-1800 mg/dl)

52. • Final diagnosis- Common variable immunodeficiency