case_images: PMC10477990_01
case_images: Clinical Course of the 117-day-old Patient with mixed infection and primary disease. (A) shows a timeline beginning with the patient's first vsit to a regional hospital in November 2018 and ending after his recovery in March 2019. Major events during the course of the patient's illness are indicated by arrows. (B) shows laboratory values obtained and pertinent medications administered during the patient's second hospitalization. The graph shows the body-temperature curve (red line) and peripheral-blood neutrophil counts (blue bars), lymphocyte counts (green bars) and other white cell count (purple bars). The horizontal thick gray lines show the medications administered. (MER denotes meropenem, CEFO denotes cefoperazone sulbactam, SMZ denotes cotrimoxazole, GAN denotes ganciclovir, IMI denotes imipenem cilastatin sodium, LIN denotes linezolid, CEFOX denotes cefoxitin, RIF denotes rifampin, TIS denotes tisoniazid, matrix-assisted laser desorption ionization-time of flight denotes MALDI-TOF.
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case_images: Fudan University in Shanghai, China, after continuous diarrhea for 2 weeks, cough for 1 week, and shortness of breath for 1 day ( Figure 1A ). Fourteen days previously, on December 1st, 2018, he visited the outpatients' department of a regional hospital for diarrhea, and his symptoms were relieved after probiotic treatment ( Figure 1A ). On December 8th, 2018, he visited the same regional hospital again for cough and expectoration and was diagnosed with pneumonia and treated with cefaclor ( Figure 1A ). Six days later, he was hospitalized with progressively severe pneumonia and respiratory failure ( Figure 1A ). After brief hospitalization in a regional hospital, the patient's progressively worsening condition so that he was transferred to the emergency department of our hospital for further evaluation and treatment ( Figure 1A ). About 17 hours later, there was no improvement of respiratory distress, so the patient was intubated and received mechanical ventilation (MV) ( Figure 1B ). C-reactive protein (CRP) was 12 mg/L, and procalcitonin (PCT) was 0.35 ng/ml. Chest X-ray and computed tomography (CT) imaging revealed extensive exudation ( Figures 2A-1, B-1 ). From the 1st day to the 5th day, his pulmonary signs did not improve and he had an intermittent fever, reaching up to 39.0 C ( Figure 1B ). BALF culture results were all negative ( Figure 1B ). The patient's body temperature returned to normal and his pulmonary infiltrates improved after his admission. Based on these above, it is considered that the evidence of M. abscessus infection is insufficient. On the 28th day, the patient developed a new onset of fever, and his body temperature rose to 40 C ( Figure 1B ). On the 34th day, the third mNGS on BALF suggested an increase sequences in M. abscessus ( Supplementary Figure 1 ,  Supplementary Table 1 ). On the 56th day, he was eventually weaned from ventilator and transferred to the immunology ward on the 60th day ( Figures 1A, B ).
case_images: Chest Imaging, Neuroradiologic CT and Fundus perforator. The images shown in (A-1), (B-1), and (C-1) were acquired on admission to the emergency department of Children's Hospital of Fudan University. Extensive exudation and parenchymal lesion of the chest was revealed (A-1, B-1, black arrows). And the image of the head was normal (C-1, white arrows). The image shown in (A-2), (B-2), and (C-2), (D-1) and (D-2) were acquired on day 14, after 10-day anti-microbial therapy. Progression of parenchymal lesion and interstitial infiltrates of the chest was revealed (A-2, B-2, black arrows), while multiple punctate calcifications of basal ganglia of the head was revealed (C-2, white arrows). Fundus examination suggested binocular leukoplakia lesions (D-1, D-2, white arrows). The image shown in (A-3) and (F) were acquired on day 36, after targeted anti-microbial for multiple pathogens. Lesions in lungs was nearly resolved (A-3, B-3, black arrows). The image shown in (D-3), (D-4) were acquired on day 72. Diffuse infiltrating lesions in his eyes and vascular white sheath were revealed (D-3, (D-4), white arrows).
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case_images: Figures 2A-2, B-2 ), and the head CT scan suggested multiple punctate calcifications of the basal ganglia ( Figure 2C-2 ). Fundus examination suggested binocular leukoplakia lesions ( Figures 2D-1, D-2 ).
case_images: Diagnosis of MHC II deficiency by Means of Unbiased NGS. (A) shows the result of whole exome sequencing. (B, C) shows the result of generation sequencing.
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case_images: In the following days, his lung lesions resolved and his temperature dropped close to normal ( Figures 2A-3, B-3 ). Fundus reexamination showed diffuse infiltrating eye lesions and a vascular white sheath ( Figures 2D-3, D-4 ). After 3 months, the results showed MHC Class II deficiency, which was caused by a heterozygous mutation in the class II major histocompatibility complex transactivator (CIITA) gene ( Figure 3A ).