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Educational draft · awaiting clinical reviewThe full textbook explains uncertainty but does not replace live national or local guidance, specialist advice, or current prescribing information.
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Primary and secondary immunodeficiency

Recognise clinically important immune failure, distinguish inherited from acquired causes, map infection patterns to immune compartments and investigate urgently without delaying treatment of active infection.

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01Core principlesThe concepts and mechanisms needed to understand the subject.

Immunodeficiency means inadequate defence against infection or immune dysregulation caused by an intrinsic immune disorder or an acquired process. “Primary” now encompasses many inborn errors of immunity and need not present in childhood. “Secondary” includes loss, suppression or consumption of otherwise intact components. The distinction matters for genetics, prognosis and family counselling, but the first clinical task is the same: recognise dangerous infection and stabilise it without waiting for a complete classification.

Patterns can localise function. Antibody defects often cause recurrent sinopulmonary infection with encapsulated bacteria and may emerge after maternal antibody wanes or in adulthood. T-cell or combined defects predispose to viral, fungal and opportunistic disease, chronic diarrhoea and failure to thrive. Phagocyte number or function defects can cause deep bacterial or fungal infection and poor wound healing. Terminal complement defects associate with invasive Neisseria, while early complement defects can combine infection with immune-complex disease. These are clues rather than one-to-one rules.

Immune dysregulation broadens the phenotype. Autoimmune cytopenia, enteropathy, eczema, granulomatous inflammation, persistent lymphadenopathy, splenomegaly and unusual malignancy can accompany an inborn disorder. Family history may show recurrent infection, early infant deaths, consanguinity or affected males, but de novo and recessive disorders can lack a clear pedigree. An unexpectedly weak inflammatory response does not reassure: certain signalling defects can produce severe bacterial infection with little fever or acute-phase response.

Secondary causes must be actively sought. Corticosteroids, cytotoxic therapy, B-cell depletion, transplantation and targeted immunomodulators create mechanism-specific and time-dependent risk. HIV affects cellular immunity; haematological malignancy can impair quantity and quality of lymphocytes and antibodies. Nephrotic or gastrointestinal protein loss lowers immunoglobulin; splenectomy weakens clearance of encapsulated organisms; malnutrition and critical illness disrupt several defences. Structural lung or urinary disease may mimic immune failure by causing recurrent infection at one site.

Investigation is layered. Document organisms, sites, severity, response, cultures, antimicrobial exposure and imaging rather than relying on the word “recurrent.” Initial tests commonly include full blood count with differential and film, quantitative IgG, IgA and IgM, renal and liver profiles, albumin and HIV testing. Further lymphocyte subsets, vaccine antibody responses, complement pathways, neutrophil function, bone marrow or genomic testing are selected with immunology input because timing, age, infection and treatment alter results.

Management matches mechanism and patient outcome. Prompt infection treatment, vaccination planning, antimicrobial prophylaxis, immunoglobulin replacement, haematopoietic transplantation or gene-based therapy may be appropriate in different disorders. Immunoglobulin replacement is specialist treatment based on diagnosis, functional antibody failure and infection burden rather than a single low value, and dosing is individualised to clinical outcomes. Protect organs through pulmonary review, microbiology, physiotherapy and surveillance while supporting genetic counselling and emergency plans.

Key points

  • Suspect immunodeficiency when infections are unusually severe, persistent, recurrent, treatment-resistant or caused by unusual organisms, rather than counting minor infections alone.
  • Primary immune regulatory disorders can present from infancy to adulthood and may cause autoimmunity, inflammation, lymphoproliferation or malignancy as well as infection.
  • Secondary causes are more common: medicines, haematological malignancy, HIV, protein loss, malnutrition, asplenia, renal disease and critical illness can impair different compartments.
  • The organism, anatomical site and age of onset suggest the affected arm: antibody, T cell, phagocyte, complement or combined immunity.
  • Begin with history, examination, full blood count and film, quantitative immunoglobulins, HIV testing with consent and targeted assessment of secondary causes.
  • Normal screening results do not exclude functional or pathway-specific defects when phenotype is strong; discuss early with clinical immunology.
  • Treat active sepsis promptly, avoid unsafe live vaccines when severe cellular immunodeficiency is possible, and coordinate prophylaxis or replacement through specialists.
02Mechanisms and patternsImportant relationships and how to distinguish them.
Serious, persistent or unusual infectionRed flag

Invasive infection, repeated hospitalisation, failure of standard treatment, opportunistic organisms or infection at multiple sites raises concern beyond ordinary frequency.

Early combined phenotypeRed flag

Thrush, chronic diarrhoea, failure to thrive, persistent viral infection or vaccine-strain disease in infancy demands urgent specialist assessment.

Antibody pattern

Recurrent bacterial ear, sinus and chest infection, bronchiectasis or Giardia can indicate impaired antibody quantity or function.

Phagocyte pattern

Deep abscesses, invasive bacterial or fungal disease, poor wound healing and abnormal neutrophil counts suggest number or function defects.

Complement pattern

Recurrent invasive meningococcal disease particularly suggests terminal pathway failure; pneumococcal disease and autoimmunity may implicate other components.

Immune dysregulation

Autoimmune cytopenia, enteropathy, eczema, lymphoproliferation, granulomas or malignancy may be the presenting face of an inborn error.

Secondary context

Immunosuppressive therapy, HIV risk, malignancy, protein loss, asplenia and malnutrition can explain an acquired phenotype and alter urgent management.

03Interpreting evidenceInformation, measurements and their limitations.
Reasoning sequence

Consider the information, its meaning and its limitations before deciding what follows.

  1. 01
    Documented infection phenotype
    Why
    Retrieve organisms, culture sites, imaging, antimicrobial courses, severity and response across records.
    Interpretation and limitations
    Repeated viral upper-respiratory symptoms differ from culture-proven pneumonia, opportunistic infection or invasive encapsulated bacterial disease.
  2. 02
    Full blood count and film
    Why
    Assess lymphocyte, neutrophil and platelet numbers and morphology.
    Interpretation and limitations
    Interpret age-specific counts and trends; acute infection and treatment can transiently alter cells, and normal counts do not prove normal function.
  3. 03
    Quantitative immunoglobulins
    Why
    Measure IgG, IgA and IgM with age-appropriate reference intervals.
    Interpretation and limitations
    Low values suggest loss, impaired production or consumption; normal totals do not exclude specific antibody dysfunction or cellular defects.
  4. 04
    Secondary-cause screen
    Why
    Use history and targeted tests for medicines, HIV, malignancy, renal or enteric protein loss, liver disease and nutrition.
    Interpretation and limitations
    A secondary explanation can coexist with an inherited susceptibility and should be linked mechanistically to the infection pattern.
  5. 05
    Functional and cellular testing
    Why
    With immunology, select vaccine responses, lymphocyte subsets, complement assays and neutrophil function.
    Interpretation and limitations
    Results depend on age, recent vaccination, infection, immunoglobulin replacement and immunosuppressive exposure. Recurrent meningococcal disease specifically warrants specialist review for complement deficiency or inhibition even when cell counts and immunoglobulins are normal.
  6. 06
    Genomic testing
    Why
    Consider NHS genomic testing when an inborn error is suspected and the phenotype meets the National Genomic Test Directory criteria.
    Interpretation and limitations
    Testing can confirm mechanism and inform relatives, but consent, variant interpretation and genetic counselling are integral to the result.
04Applied reasoningWorked examples connecting principles to decisions.
01Worked caseAdult recurrent pneumoniaA 38-year-old has three radiologically confirmed pneumonias in two years, chronic sinusitis and low globulin; there is no known childhood diagnosis.
  1. 1Assess current infection severity and treat promptly, while building a verified timeline of organisms, sites, imaging, antibiotic response and structural lung damage.
  2. 2Recognise an antibody-pattern phenotype that can present in adulthood, but review secondary causes including B-cell-active medicines, haematological disease, HIV risk and protein loss.
  3. 3Order initial full blood count with film, quantitative immunoglobulins, renal and liver profiles, albumin and consented HIV testing, and discuss early with clinical immunology before unstructured panels.
  4. 4Verify abnormalities when clinically appropriate, arrange specialist functional testing and pulmonary assessment, and base prophylaxis or replacement on diagnosis and infection outcomes rather than one concentration.
02Emergency approachInfant with possible combined immunodeficiencyA four-month-old has persistent thrush, chronic diarrhoea, failure to thrive and severe viral lower-respiratory infection.
  1. 1Stabilise and treat the active infection with paediatric infectious-disease and critical-care input as needed.
  2. 2Recognise an urgent combined immune phenotype and protect the infant from avoidable live-vaccine or transfusion-related risks through specialist protocols.
  3. 3Obtain age-interpreted blood count and directed immune studies while contacting paediatric immunology and genomics; do not delay referral for a normal total white count.
  4. 4Confirm a definitive pathway rapidly, communicate infection-control and blood-product requirements, and begin mechanism-specific definitive planning with the family.
03Applied approachRecurrent infection with normal screeningA young adult has invasive meningococcal disease twice but normal immunoglobulins and lymphocyte counts.
  1. 1Verify episodes and microbiology and assess immediate infection and public-health requirements.
  2. 2Recognise that normal antibody concentrations and cell counts do not assess the terminal complement pathway.
  3. 3Discuss targeted complement functional testing and alternative anatomical or acquired causes with immunology.
  4. 4After confirmation, implement the specialist vaccination, prophylaxis, education and family-assessment plan and verify adherence and breakthrough events.
05Checking understandingVerify the reasoning, revisit uncertainties and apply feedback.
  • Maintain an infection diary with organism, site, severity, treatment, cultures and outcome to judge disease activity and treatment effect.
  • Trend blood counts and immunoglobulins in relation to infections, protein loss, immunosuppressive exposure and replacement therapy.
  • Monitor organ damage, especially bronchiectasis, hearing, growth, nutrition and gastrointestinal disease, through the relevant specialty plan.
  • For immunoglobulin replacement, specialists individualise route, dose and target to infection burden and adverse effects rather than chasing one universal trough.
  • Review vaccination and household protection with immunology, avoiding live vaccines when contraindicated and checking current Green Book advice.
  • Update genetic counselling, family testing and transition plans as molecular classification and family circumstances evolve.
06Special situationsVariants, exceptions and circumstances that change the usual approach.

Age does not exclude primary disease

Hypomorphic variants, antibody disorders and immune dysregulation can first become apparent in adolescence or adulthood.

Frequency is less discriminating than quality

One opportunistic or invasive infection may be more informative than many self-limited colds in a high-exposure setting.

Inflammation may be muted

Some signalling defects and immunosuppressive states produce severe infection without expected fever or biomarker elevation.

Normal quantity can hide dysfunction

Normal immunoglobulin, complement or neutrophil counts do not guarantee effective antigen response, pathway activation or killing.

Treatment distorts testing

Recent immunoglobulin replacement, transfusion, vaccination, steroids and B-cell depletion can make functional and serological results difficult to interpret.

Genomics needs phenotype

A broad test is most useful when linked to detailed infections, immune studies and family structure; a variant alone may not establish causation.

Secondary and primary can coexist

An inherited vulnerability may become clinically visible only after a medicine, malignancy or physiological stress reduces reserve.

07Common pitfallsFrequent interpretation and management errors.
  1. 01

    Reassuring from the number of infections without checking severity, organisms, sites and treatment response.

  2. 02

    Assuming primary immunodeficiency always presents in childhood or always has a family history.

  3. 03

    Ordering broad immune panels before documenting phenotype and excluding common secondary causes.

  4. 04

    Using adult lymphocyte reference intervals in infants or ignoring transient treatment effects.

  5. 05

    Giving a live vaccine while severe T-cell immunodeficiency remains plausible without specialist advice.

  6. 06

    Starting long-term immunoglobulin from one low result without functional assessment, infection outcomes and specialist oversight.

Practice

Two practice questions

Question 1 of 20 correct
Clinical foundationsOriginal SBA

Pattern-directed assessment

A 38-year-old has recurrent radiologically confirmed bacterial pneumonias, chronic sinusitis and a low globulin concentration. Which is the best initial approach?

Sources and review status5 sources · checked 7 Sept 2026 · clinical review pending
Sources

Sources and review status

National guidance is shown before implementation-dependent detail. Apply principles in context and verify current guidance when a decision affects care. Source check completed 7 Sept 2026; clinical approval remains outstanding.

Authoring stateComplete draftClinical stateAwaiting reviewJurisdictionUnited Kingdom