Autosomal dominant IFN-γR1 deficiency presenting with both atypical mycobacteriosis and tuberculosis in a BCG-vaccinated South African patient

To the Editor,

Mendelian susceptibility to mycobacterial disease (MSMD) refers to a group of primary immunodeficiency disorders (PIDs) that characteristically cause susceptibility to mycobacterial infections by a range of mycobacteria and to systemic non-typhoidal salmonellosis [1,2]. MSMD sufferers are also vulnerable to the more pathogenic Mycobacterium tuberculosis (TB) [3]. To date, the disruption of IFN-γ immunity has been reported in all genetic etiologies of MSMD [2,12,13]. The prevalence of MSMD is currently unknown in South Africa and is almost certainly masked by the enormous TB/HIV epidemic [1,14]. Poor awareness of PID adds to the lack of or late diagnosis. Age of onset of MSMD reported from regions of lower prevalence of TB is typically in infancy with disseminated infection by weakly virulent mycobacteria such as BCG or atypical mycobacterial species. MSMD clinical presentation and the virulence of the infecting organism in highly endemic regions has only rarely been reported on [2,15].

Here we describe a girl of South African mixed ethnicity (with genetic contributions from Khoesan, Bantu-speaking Africans, European, and Asian ancestors [16]) of non-consanguineous parents who was referred at age 9 years from an orthopaedic facility to the Paediatric Rheumatology Service, Tygerberg Hospital. She was severely wasted and wheelchair bound with chronic arthritis of her left ankle. She had not responded to extended antibacterial treatment for suspected staphylococcal septic arthritis nor to completed 6 months of standard anti-tuberculous treatment. Her sputum was positive for Ziehl Neelsen (ZN) stain for acid fast bacilli (AFB), but culture negative. Owing to the lack of response she had been started just prior to referral on 18-months treatment for suspected drug resistant TB, with initial ZN negative sputum but subsequent positive cultures of both TB and non-tuberculous mycobacteria (MOTT) -resembling Mycobacterium avium subsp intracellulare (MAI) -from sputum and neck lymph nodes. These had been PCR-confirmed, with corresponding adjustment of therapy. Granulomatous tissue had been identified on histology of the ankle joint, but no AFB were seen, and culture was negative for TB. She had been vaccinated with Bacillus Calmette–Guérin (BCG) at birth, as evidenced by scarring on her upper arm. At 6 months, according to maternal history, she had been treated for pulmonary TB in a rural hospital of the Eastern Cape Province of South Africa. There was no relevant history of other infections, no family history of recurrent infections with either TB, MOTT, or Salmonella. The patient has three, healthy, live siblings. The family lived in an informal settlement on the outskirts of Cape Town.

On examination at presentation to the Rheumatology Clinic, there was no evidence of syndromic features, specifically none of ectodermal dysplasia. The patient was severely wasted with a weight of 19.8kg (3^rd centile for age) and length 142cm (25^th centile) at age 9 years. Severe mono-arthritis of the left ankle joint was noted, which prevented the patient from walking unassisted. Despite 6 weeks of intensive antibiotic treatment for presumed septic arthritis (S. aureus cultured from a tissue biopsy) and 6 months of TB therapy, there was poor response of both the arthritis and still severe wasting. She was started on a five-drug regime for MAI as soon as a culture positive sputum sample was obtained for a non-TB organism presumed MAI.

On baseline investigation, HIV Elisa test was negative. Erythrocyte sedimentation rate (ESR) was 115mm/hr and remained elevated on repeated determinations. She had normal lymphocyte subset and total numbers. Neutrophils were elevated: 14.34 (N 1.4–5.2×10>9/L), Immunoglobulins were normal, neutrophil burst showed normal response. There was no record of a Tuberculin Skin Test (TST) on the initial workup of the patient. Lymphocyte proliferation response to Phytohaemagglutinin (PHA), Concanavalin A (ConA) and Pokeweed mitogen were normal. Lymphocyte proliferation response to Protein A and Candida stimulation were reduced compared to adult control. A commercial IFN-γ release assay was not locally available at the time. On chest X-ray (Figure 1A), there was evidence of scattered lytic lesions in the humerus and clavicle. Multiple abnormal uptake areas or “hot spots” were reported on radio-nucleotide bone scan (Figure 1B).

Figure 1.

(A) Chest X-ray of the patient. White arrow indicates lytic lesions in the humerus. (B) Bone scan of the patient. Multiple small radio dense lesions demonstrated in the bones (indicated by the black arrows).

The patient gradually improved on her treatment for MOTT in the time leading up to a defined diagnosis. However, she defaulted follow up at age 12 before further consideration of specific treatment options for MSMD. She re-entered medical care aged 15 years with admission to a neighbouring academic hospital, with left leg chronic pain, weight loss and night sweats. CT scan showed multiple small radio-dense lesions in liver, brain, bones and lungs (Figure 1B). Bone biopsy culture confirmed MAI. She was again started on 18-months of MOTT therapy and antibiotic prophylaxis. She defaulted from care until a further relapse of her symptoms. Challenges with compliance and accessing care despite intensive counselling, have prevented optimal management including surveillance and prophylactic antibiotics for TB and potential adjunctive treatment strategies such as IFN-γ therapy.

The study was approved by the Health Research Ethics Committee of Stellenbosch University (study no. N08/09/264). The mother granted informed consent, and this included the genetic evaluation of the affected individual, her brother and her half-sister. Additionally, informed consent was also obtained from both parents as well as two healthy control individuals. The study adhered to the ethical guidelines as set out in the Declaration of Helsinki, 2013 [17].

Cells from the patients responded modestly to IFN-γ by whole blood assay [18] and EMSA, whereas their response to IL-12 and IFN-α was normal, highly suggestive of a defect in IFN-γ signaling pathway (Supplementary Table 1 and Supplementary Figure 1). Sanger sequencing of all exons of IFNGR1 in the family members identified a de novo heterozygous four base pair deletion in exon 6 of IFN-γR1 at nucleotide 818 (818del4) in the affected individual (Supplementary Figure 2). This mutation has previously been identified in individuals with MSMD, and is responsible for an impaired response to IFN-γ [19] due to the accumulation of IFN-γR1 at the cell surface (Supplementary Figure 3), lacking the recycling motif, leading to a dominant negative effect on the WT. This mutation was the first identified hotspot of small deletion in humans, discovered in patients with MSMD and was previously identified in patients with TB [20,21]. Together, these results suggest that the patient has AD IFN-γR1 deficiency leading to a poor response to IFN-γ and TB.

The case we present here represents the first confirmed diagnosis from South Africa of a mutation of a MSMD gene, with recurrent infection with TB and other less pathogenic mycobacteria. The infection with both environmental and typical mycobacteria as well as negative HIV status, focusses attention on a genetic etiology. Despite the high prevalence of TB or in fact especially in areas of high TB prevalence, genetic causes of TB should be considered. Genetic predisposition in these high infection pressure settings will elucidate the intricate pathways of the immune response to TB. Therefore a genetic cause should be considered in all children and adults HIV negative with severe, persistent, unusual or recurrent mycobacterial disease.

Supplementary Material

Supplementary Figure 1

Supplementary Figure 1. Impaired response to IFN-γ in the patient’s EBV-B cells. IFN γ and IFN-α responses were tested by EMSA in patient’s EBV B cells and compared with the response of a healthy individual EBV B cells (C+). The cells were either not stimulated or stimulated with two doses of IFN-γ and IFN-α (103 and 105 UI/ml, respectively). Nuclear proteins were extracted and loaded on a gel with a GAS probe.

Supplementary Figure 2

Supplementary Figure 2. Identification of the mutation in exon 6 of IFN-γR1. All flanking intronic regions and exons of IFN-γR1 were Sanger sequenced. The heterozygous mutation 818del4 (black open rectangle), a previously identified heterozygous mutation, was identified in the patient’s gDNA.

Supplementary Figure 3

Supplementary Figure 3. Increased cell surface expression of IFN-γR1 in EBV-B cells of the patient. Cell surface expression of IFNGR1 on EBV B cells from three healthy individuals (WT/WT1, WT/WT2, and WT/WT3), the patient (818del4/WT) and a patient (RC-R1) with AR complete IFN-γR1 deficiency without expression detected by flow cytometry.