Case 3

Immunopathology And Microbiology

Case 3:  Severe Combined Immune Deficiency

  • Contributed by Tisha Foster, MD and Keeta Gilmore, PhD
    Department of Pathology, University of Oklahoma Health Sciences Center
  • Published on-line in November 2003

Clinical History: 

The patient is a 6 month old white male with a 2 month history of persistent cough who was treated with various antibiotics, but showed no improvement.  He was subsequently admitted to Children's Hospital with respiratory distress, pneumonia with extensive bilateral pulmonary infiltrates, and impending respiratory failure of unknown etiology. 

Laboratory Data: 

The white blood cell count was elevated at 40 K/mm3 with a neutrophilic leukocytosis and relative lymphopenia.  Chemistries reflected normal renal and hepatic function.  A cardiac ultrasound was normal. 


A nasopharyngeal wash and swab were performed and tested for direct fluorescent antibodies to adenovirus, influenza A and B, parainfluenza and RSV.  These were all negative.  A viral culture was also performed and no virus was isolated.  A bronchoalveolar lavage was performed and the following cultures were negative:  Legionella, Mycoplasma, fungal, AFB, CMV, Chlamydia, and Bordetella pertussis.  A bacterial culture grew Enterobacter cloaceae and a direct fluorescent antibody to Pneumocystis carinii was strongly positive.

Figure 1 - 40x

Figure 2 - 100x

Figure 3 - 40x

Figure 4 - 100x

The monoclonal antibodies in the MONOFLUO test kit are chemically linked to fluorescein isothiocyanate (FITC) to produce a highly specific, direct, immunofluorescent reagent with a low level of background fluorescence.  In addition to binding withPneumocystis carinii cysts, the monoclonal antibodies also bind specifically to Pneumocystis carinii trophozoites, sporozoites, and the extracellular matrix.  Specimens infected with Pneumocystis carinii contain large round-to-elliptical shaped cysts, found both individually and in clusters, which will be stained bright apple-green.  Sporozoites and trophozoites may also be stained, appearing as relatively small, crescent-shaped or pleomorphic structures.  In addition, the amorphous extracellular matrix should also fluoresce brightly.  Other organisms and cellular material from respiratory specimens are counterstained red to orange-red or gold without characteristic fluorescence of Pneumocystis carinii cysts. 

Other labs:

Test Result Reference Range
Anti-HIV 1/2 negative  
HIV-1 ultra-sensitive PCR RNA negative  
IgG >45 231-1411mg/dL
IgA 12 0-83 mg/dL
IgM 18 0-145 mg/dL
IgD 0 0-14 mg/dL
IgE >2 0-158 IU/ml

Flow Cytometry:

Marker % Reference Range Marker % Reference Range
CD2 4 55-88% CD19 96 13-35%
CD3 3 50-77% CD20 96 2-34%
CD4 2 33-58% Kappa chain 51 50-70%
CD5 2 47-95% Lambda chain 35 30-50%
CD8 1 13-26%  

More results:

A test for ADA deficiency was performed at the Oklahoma Medical Research Foundation (OMRF) and the patient was not found to be deficient in adenosine deaminase.  He was then transferred to Duke for further workup and bone marrow transplant.


Severe combined immunodeficiency


Severe combined immunodeficiency (SCID) is a heterogeneous group of genetically distinct disorders representing the most severe forms of primary immunodeficiency which are characterized by variable abnormalities of T, B, and natural killer cell development and function.  These entities arise from a variety of molecular defects, and the deficits in both cell-mediated and humoral immunity lead to similar presentations in all the defined conditions.  The incidence ranges from 1 in 30,000-70,000 live births.  Clinical presentation includes oral candidiasis, skin rashes, failure to thrive, chronic diarrhea, and recurrent severe infections by a wide range of pathogens (including Candida albicans, Pneumocystis carinii, Pseudomonas, CMV, varicella, and numerous bacteria) generally within the first 3-6 months of life when the protective effect of maternally transmitted immunoglobulin has diminished.  Frequently the first indication of SCID is pneumonia with an opportunistic organism, such as Pneumocystis carinii or CMV.  Pneumocystis carinii is the most common respiratory infection in SCID and is often found as a co-pathogen with a respiratory virus.  Chest radiographs may show absence of a thymus, hyperinflation of lungs, and interstitial pneumonitis.  Peripheral blood examination demonstrates an absolute lymphopenia of >500 per microliter with a marked reduction in mature T cells and a more variable decrease in   cells associated with hypogammaglobulinemia and lack of specific antibody response to immunization. 

Immunoglobulin measurement may or may not help in diagnosis due to normal IgG concentration secondary to maternal origin.  Infants with SCID usually have less than 15% T cells (CD3).  Serum concentrations of IgG, IgM, and IgA are reduced, and children are unable to from specific antibody.  Low absolute lymphocyte count is the most important clue to diagnosis.  Unless treatment with bone marrow transplantation or enzyme replacement therapy occurs, death usually occurs before the patient's first birthday. 


Analysis of the immunological profile can provide an indication of the nature of the underlying genetic abnormality.  Nearly all cases of SCID have very low or absent numbers of T lymphocytes.  Patients are then grouped into those who have B lymphocytes and those who do not.  Further subclassification can then be made according to the presence or absence of natural killer cells. 

The X-linked form of SCID is the most common form, accounting for 50-60% of cases.  The abnormal gene has been mapped to Xq13 and the genetic defect is a mutation in the common gamma chain subunit of several cytokine receptors (IL-2, 4, 7, 9, and 15).  Lymphoid progenitor cells fail to be stimulated by these cytokines, resulting in an absence of T and NK cell development but normal B cell numbers. 

The form of SCID resulting from the adenosine deaminase deficiency (ADA deficiency) is the most common cause of autosomal recessive SCID  which is found in 20% of all SCID cases and in 30-50% of patients with autosomal recessive SCID.  The gene for ADA is located on chromosome 20q.  Adenosine deaminase catalyzes the irreversible deamination of adenosine to inosine and of 2'-deoxyadenosine to 2'-deoxyinosine.  ADA deficiency leads to accumulation of adenosine and 2'-deoxyadenosine and its derivatives which are toxic to immature lymphocytes, especially those of T lineage. 


Treatment of this disease is determined by the pathogenesis of the disorder.  Specific antibiotic treatment is given for infections, including prophylaxis for Pneumocystis carinii and fungal infections.  Patients should not receive live vaccine.  All blood products must be irradiated to avoid graft-versus-host disease and the condition is best treated by a histocompatible bone marrow transplantation.  Most are also treated with IV immunoglobulin until bone marrow engraftment is complete.  Patients with ADA deficiency are candidates for either bone marrow transplantation from an HLA-identical or haploidentical donor or enzyme replacement therapy with polyethylene glycol (PEG)-conjugated bovine ADA.  Gene therapy has also been used successfully in a few patients.  The ADA gene may be introduced into the patient's bone marrow cells before reinfusion, or T cells harvested from the patient are transfected with the ADA gene and returned to the patient. 

SCID is a curable condition.  After successful bone marrow transplantation, most patients lead entirely normal lives with a fully functioning immune system, or at worst need weekly IV immunoglobulin replacement.  Early diagnosis is vital, otherwise patients rapidly succumb to infection before curative bone marrow transplant can be performed. 


  1. Gennery AR, Cant AJ. Diagnosis of severe combined immunodeficiency. Journal of Clinical Pathology 2001; 54(3):191-5. 
  2. Gaspar HB, Gilmour KC, Jones AM. Severe combined immunodeficiency - molecular pathogenesis and diagnosis.Archives of Disease in Childhood  2001; 84(2):169-73.