Our patient is a 3-year-old Pakistani female born to first-degree cousins. She presented at the age of 10 months with enlarged cervical lymph nodes and diarrhea. She had multiple admissions for recurrent diarrheal illnesses. The diarrhea started at the age of 7 days, with a frequency of more than 10 times per day of watery consistency but no blood or mucus. She was started on an elemental amino acid-based formula because of a diagnosis of food protein-induced enterocolitis syndrome based on a presentation of severe bloody diarrhea, acidosis and hypotension. She had a sister who had a similar presentation of chronic diarrhea and fever and died at the age of 1 year due to septic shock. Immune deficiency was not suspected and the underlying cause was not investigated. Also, no genetic tests were obtained and the family did not receive any prenatal genetic counseling.
After removing cow's milk from our patient's diet and initiating the special formula, her diarrhea settled, but at the age of 1 year, she had a recurrence of diarrhea described as bloody and associated with multiple perianal abscesses. The abscesses were treated with intravenous antibiotics and surgically drained. The culture from the drained pus repeatedly grew extended spectrum beta-lactamase-producing E. coli and Klebsiella species. At the age of 2 years, she developed arthritis involving large joints of the lower limb (knees and ankle) and wrist associated with morning stiffness and an inability to walk.
On examination, the patient had severe failure to thrive. Multiple enlarged cervical lymph nodes were noted. The scar of the Bacillus Calmette-Guerin (BCG) vaccine was normal, and no axillary lymph nodes were detected. The liver was palpable 3 cm below the costal margins. She had swelling of the left knee joints with a reduced range of movement. Perineal examination revealed inflammation, multiple scars of drained perianal abscesses and a perianal fistula opening (Fig. 1). 
Laboratory investigation revealed leukocytosis (29.1 x 109/L), anemia (hemoglobin 8.4 g/dL), elevated inflammatory markers (C-reactive protein 12.0 mg/dL, and ESR 80 mm/h) and elevated immunoglobulin levels. A rheumatological workup was positive for serological markers of autoimmunity, including antinuclear antibodies (ANA) (titer 1:80, speckled pattern), rheumatoid factor (25.1 IU/mL; normal < 15), anti-cyclic citrullinate peptide (anti-CCP) antibody titer (216.7 u/mL; normal < 20) and anti-double-stranded DNA (anti-dsDNA) antibodies (83.6 IU/mL; normal < 35). In addition, these markers were positive on repeated testing. Other markers, including anti-RNP, anti-SSA, anti-SSB, and anti-Sm, remained negative, while C3 and C4 complement levels were not suppressed. Joint fluid sampling was obtained, and an infectious etiology for joint involvement was excluded by culture obtained from the knee joint. Based on the clinical presentation and laboratory workup, a diagnosis of oligoarticular juvenile idiopathic arthritis (JIA) was provided.
Furthermore, microbiological testing for infectious diarrhea, including stool culture and sensitivity tests, a stool ova and parasite examination, Clostridium difficile toxin test, and Giardia lamblia and Cryptosporidium stool antigen tests, were negative. The celiac panel was also negative, and malabsorption tests, including fecal fat and fecal elastase tests, were normal. Stool examination was positive for fecal occult blood, and fecal calprotectin, an indicator of intestinal inflammation, was elevated at 580 mcg/g (normal < 50.0). Workup for TB was negative, including bone marrow and lymph node examination, using polymerase chain reaction (PCR) assay, cultures, and the TB gold test. In addition, a purified protein derivative (PPD) skin test was performed on the patient and showed no reaction.
In view of her presentation and the early colitis symptoms, she was further evaluated, and a diagnosis of CGD was made based on the oxidative burst assay [dihydrorhodamine-1,2,3 (DHR) flow cytometry test], which revealed an absence of NADPH oxidase activity in the patient's neutrophils upon phorbol myristate acetate (PMA) stimulation (Fig. 2). The neutrophil oxidative index (NOI) of the patient was < 5. NOI measures the oxidative ability of phagocytes and their overall integrity and is calculated from the ratio of the fluorescence in stimulated phagocytic cells to the fluorescence expressed in unstimulated phagocytic cells. The normal value in control specimens is usually > 73. 
The diagnosis of CGD was confirmed by targeted next-generation sequencing using Ion AmpliSeq Designer software (Life Technologies, Carlsbad, CA, USA). The gene panel used analyzed over 200 genes associated with immune deficiency and immune dysregulation, including auto-Inflammatory and Autoimmunity syndromes. The test was performed on venous blood samples collected in EDTA tubes for DNA extraction after obtaining written consent from the parents to perform the genetic diagnostic assay. The test revealed a deletion mutation in exon 10 as a homozygous loss-of-function variant of NCF2 (NCF2: NM_001190789, nucleotide change: c.855_856del:p.T285fs). Both parents were heterozygous for the mutation. We believe this to be a novel variant that has not been previously reported.
To prevent serious and life-threatening infections, the patient was started on an antibacterial and antifungal prophylactic regimen consisting of trimethoprim-sulfamethoxazole (trimethoprim 6 mg/kg/day) and itraconazole (5 mg/kg/day), respectively. She remained free of infection. Her arthritis symptoms were initially managed with naproxen followed by oral prednisolone at a dose of 1 mg/kg/day for 4 weeks followed by gradual tapering and then discontinued after 4 months. In addition, hydroxychloroquine was initiated and continued throughout the observation period, which lasted for 18 months following the onset of arthritis. She showed improvement and started to walk with no pain and had no relapse of symptoms during subsequent follow-up visits. However, we failed to establish long-term follow-up. In addition, further endoscopic, histological and imaging studies were planned but not performed because the patient and family traveled to their home country and were lost to follow-up.