Indian Rheumatology association

Infection Susceptibility in Inborn Errors of Immunity: Pattern-based Approach

Dr Murugan Sudhakar

Associate Professor,
Division of Pediatric Clinical Immunology & Rheumatology,
Christian Medical College, Vellore, India

Inborn Errors of Immunity (IEI), formerly known as Primary Immunodeficiency Disorders (PID), encompass a spectrum of conditions characterised by recurrent infections, autoimmunity, autoinflammation, allergies, and malignancies. Contrary to the traditional belief that IEIs/PIDs primarily affect young children, recent evidence highlights their relevance in adults as well. Table 1 outlines common misconceptions related to the suspicion and diagnosis of IEIs/PIDs. In this letter, I will discuss a pattern-based diagnostic approach to specific IEIs, focusing on the characteristic infection patterns associated with each.

The classical teaching of PIDs into 4 major subgroups still holds its value today. It is divided into predominant B-cell defects, predominant T-cell defects, Granulocytic (neutrophil) defects, and Complement deficiencies. Clinical pattern recognition comprises age, the system affected, and the organisms involved. Table 2 summarises the pattern recognition steps for diagnosing PIDs [Common PIDs, though the list is not exhaustive], using age, infection patterns, and microorganisms. Although age usually aids in classifying/diagnosing certain types of PIDs, hypomorphic variants may present at any age.

With the discovery of more IEIs/PIDs, as well as an expanding understanding of innate immune defects and the role of auto-cytokine antibodies (phenocopies of PIDs), the relationship between specific pathogens and PIDs has become increasingly complex, not as simple as illustrated in Table 2. Table 3 provides an expanded overview of the most common pathogens and their associated PIDs. However, it is crucial to interpret these associations within the appropriate clinical context. Diagnosis should not rely exclusively on the identification of causative organisms; rather, a comprehensive clinical, necessary lab assessment remains vital. For example, certain opportunistic infections are frequently seen in intensive care settings, and adults with diabetes or secondary immunodeficiency are susceptible to specific infections: factors that must always be considered during evaluation.

Table 1: Common misconceptions

Myth

Brief Rationale/ Justification

PIDs are rare

~1 in 1200-10000 persons might have PIDs (US survey)

PIDs are very rare in adults

ESID registry (16,486 patients): Two-thirds had first symptoms before 6 years of age, but about a quarter first developed symptoms in adulthood

PIDs should have repeated infections

Infection is the commonest presentation but not universal:

ESID registry (16,486 patients): Infections alone (68%); however, if only repeated infections alone are considered to suspect PIDs, we might miss 25% of patients with PIDs

PIDs need complex/extensive laboratory tests to diagnose

Initial detection uses basic, widely available tests; complex testing is needed mainly for confirmation

Table 2: Pattern recognition

 

Defect Type

Age of Onset

Pattern of Infection

Key Organisms

T Cell Defect

2–6 months

Oral candidiasis; viral and opportunistic infections

Bacteria, mycobacteria, viruses, Fungal, Pneumocystis (opportunistic infections)

B Cell Defect

Starts by 5–7 months → adulthood

Recurrent sinopulmonary/GI mucosal infections

Predominant humoral bacteria (encapsulated bacteria), Mycoplasma, enterovirus, Giardia

Granulocyte Defect

Early/neonatal

Skin infections; lymphadenitis/abscess; deep-seated abscesses; stomatitis; perianal infections

Catalase-positive organisms: Staphylococcus, Klebsiella, Burkholderia, Candida, Aspergillus, Serratia, Nocardia

Complement Defect

Any age

Meningitis; bacteremia; pneumonia; invasive infections

Capsulated organisms: Pneumococcus, Neisseria

 
Table 3: Signature-Microorganism Based Pattern Recognition of Inborn Errors of Immunity
 

Signature microorganism / infectious phenotype

Predominant IEI

Chronic/recurrent Candida of nails, oral cavity, skin or genital mucosa

STAT1 GOF; AIRE/APECED; STAT3-HIES; IL12RB1/IL12B; CARD9

Consider broader combined immunodeficiency if accompanied by multiple viral/opportunistic infections

Invasive Aspergillus

CGD; CARD9 deficiency; severe congenital neutropenia and combined immunodeficiencies.

Staphylococcus aureus recurrent skin/deep abscesses, lymphadenitis or osteomyelitis

CGD; STAT3-HIES; severe congenital neutropenia [Pseudomonas also]; LAD; IRAK4/MyD88 pathway defects.

Disseminated BCG / environmental mycobacteria / NTM

MSMD (IL12/IFN-γ axis: IFNGR1/2, IL12B, IL12RB1, STAT1, IRF8, ISG15, etc.); GATA2 deficiency; Idiopathic CD4 lymphocytopenia; severe CID/SCID; NEMO; selected CGD.

Invasive/non-typhoidal Salmonella

MSMD/IL12–IFN-γ pathway defects; CGD; some combined immunodeficiencies.

CMV—severe, persistent or disseminated disease

SCID/CID; combined T-cell defects; GATA2 and selected immune-dysregulation disorders.

Extensive/recalcitrant HPV warts

WHIM (CXCR4); DOCK8 deficiency; GATA2 deficiency; epidermodysplasia verruciformis-associated IEI; selected combined immunodeficiencies.

Severe EBV disease, EBV-HLH or EBV-driven lymphoproliferation

XLP1/SH2D1A; XIAP/BIRC4; CD27/CD70; MAGT1; ITK; CTPS1; RASGRP1; CORO1A and related T/NK-cell defects.

HSV-1 encephalitis in a previously healthy child

TLR3 pathway and CNS-intrinsic antiviral defects: TLR3, UNC93B1, TRAF3, TBK1, IRF3, and related pathways.

Endemic Mycoses (Histoplasma, Coccidioides, Blastomyces)

MSMD; STAT3 deficiency; STAT1 GOF

 

Cryptococcus neoformans

GATA2 deficiency; STAT3-HIES; Autoantibodies against IFN- or GM-CSF; Idiopathic CD4 lymphocytopenia

Cryptosporidium parvum

Few HIGM; SCID; MHC Class II deficiency

 

Suggested Readings:

  1. Bousfiha AA, Aksentijevich I, Poli MC, Tangye SG, Al-Herz W, Aiuti A, et al. The 2024 update of IUIS phenotypic classification of human inborn errors of immunity. J Hum Immun. 2025;1(1):e20250002.
  2. Echeverri EV, Sullivan KE, Meyts I, Cunningham-Rundles C, Holland SM, Picard C, et al. Clinical pearls and pitfalls in inborn errors of immunity: an expert-derived framework for diagnostic pattern recognition. J Allergy Clin Immunol. 2026;157(2):311-325.
  3. Grumach AS, Goudouris ES. Inborn Errors of Immunity: how to diagnose them? J Pediatr (Rio J). 2021 Mar-Apr;97 Suppl 1(Suppl 1):S84-S90. doi: 10.1016/j.jped.2020.11.007.