A 22-year-old female patient was admitted to West China Hospital of Sichuan University on August 16, 2021, for chronic intermittent fever (temperature ranging from 38 to 39 C) and systemic enlargement of the lymph nodes with no obvious cause; these symptoms had occurred for over a 2-year period. In addition, the patient suffered from chills, dizziness, headache, fatigue, muscle aches, and numbness in all four extremities. The patient had visited other hospitals multiple times, but the cause of the fever and systemic enlargement of the lymph nodes was not successfully identified. This patient was administered cefoperazone sodium and sulbactam sodium via injection as first-line antimicrobial therapy; however, this treatment showed poor therapeutic efficacy. Further, the patient was later admitted to a local hospital for gradual renal impairment and was diagnosed with uremia, Sjogren's syndrome, bilateral renal atrophy, and antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis. She subsequently underwent a left nephrectomy. However, after surgery, she still experienced recurrent fever and systemic enlargement of the lymph nodes. She then visited our hospital for a clear diagnosis and further treatment. She was conscious on admission, with a body temperature of 37.3 C, and displayed no rashes or subcutaneous hemorrhage. A firm, mobile, and nontender lymph node of approximately 2 cm in diameter, with no adherence to the surrounding tissues, was palpable in the right supraclavicular area. Local redness and swelling of the skin were not observed. Routine blood examination revealed the following: red blood cell count, 2.66 x 1012/L; hemoglobin level, 81 g/L; packed cell volume, 0.26 L/L; white blood cell count, 5.47 x 109/L; platelet count, 147 x 109/L; and ferritin level, 1042.00 ng/mL. Renal function tests revealed the following: urea level, 10.8 mmol/L; creatinine level, 578 micromol/L; estimated glomerular filtration rate, 8.28 mL/min/1.73 m2; and procalcitonin level, 0.97 ng/mL. Further, immunological examination revealed the following: absolute CD4 count, 469 cells/microL; absolute CD3 count, 994 cells/microL; absolute CD8 count, 424 cells/microL; immunoglobulin G level, 29.40 g/L; immunoglobulin A level, 5910.00 mg/L; complement C3 level, 0.7120 g/L; rheumatoid factor level, 137.00 IU/mL; antinuclear antibody level, + 1:1,000 granular cytoplasm; anti-SS-A antibody, ++; and anti-Ro-52 antibody, ++. Sputum tested using the GeneXpert system (Cepheid, Sunnyvale, CA, USA) was negative for M. tuberculosis infection although the interferon-gamma release assay showed a positive result (89.49 pg/mL). In addition, a color Doppler ultrasound of the lymph nodes showed structurally abnormal and enlarged lymph nodes in the right supraclavicular area and left neck root area. Further, a color Doppler ultrasound of the urinary system revealed left renal agenesis, right renal atrophy, and the presence of parenchymal lesions in the right kidney. Abdominal computerized tomography (CT) imaging confirmed left renal agenesis and right renal atrophy (Figure 1). The CT imaging of the chest showed pulmonary bullae on the apex of the right lung and right pneumothorax, with approximately 15% compression of the right lung. An increased number of enlarged lymph nodes were also observed in the left axilla and mediastinum (Figure 2). We also subjected a kidney tissue sample from the patient (obtained from the previous hospitalization) to pathological examination at our hospital. The histological results showed the infiltration of a large number of mixed inflammatory cells into the renal interstitium, the presence of noncaseating granulomas in the focal areas, and thickening of the walls of the glomerular capsules as well as small renal blood vessels (Figure 3).
On August 24, 2021, this left kidney section was further subjected to metagenomic next-generation sequencing (mNGS) for pathogen identification. The sample was first subjected to sample enrichment via centrifugation at 15,000 g for 10 min at 4 C. Thereafter, microbial DNA was extracted from 200 microL of the enriched sample and purified via the magnetic bead method (Magen Biotechnology, Guangzhou, China). The extracted DNA was then used to construct a metagenomic library (library size: ~300 bp) according to the instructions of the Nextera XT library building kit (Illumina, San Diego, CA, USA). Next, the library size was analyzed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and quantified via qPCR (Bio-Rad CFX96, Hercules, CA, USA). After mixing the library with different index adapter sequences in equal amounts, high-throughput sequencing was performed using the Illumina NextSeq 550DX sequencing platform (San Diego, CA, USA; sequencing strategy: SE75). The data obtained were filtered using FastQC software, and valid sequences (clean reads) were obtained after removing joints, low-quality bases, and very short sequences. Bowtie2 was used to align the clean reads with the human genome reference sequence (version GRCh38), to remove host-related reads, and for optimization. The test showed the presence of M. xenopi (15 specific reads), Pseudomonas aeruginosa (27 specific reads), Bacteroides fragilis (18 specific reads), Streptococcus pneumoniae (13 specific reads), Fusobacterium mortiferum (9 specific reads), and Lodderomyces elongisporus (9 specific reads) (Table 1).
After hospitalization, the patient's body temperature fluctuated between 37.0 C and 39.5 C. A routine blood examination was repeated on September 5, 2021, which revealed a red blood cell count of 2.54 x 1012/L, hemoglobin level of 78 g/L, and packed cell volume of 0.25 L/L. Pharmacological treatment with 450 mg rifampicin once a day, 250 mg clarithromycin twice a day, and 0.75 g ethambutol hydrochloride three times a week (oral administration after hemodialysis) was initiated on September 7, 2021. After 3 days, the patient's body temperature returned to the normal range. During the 4-month follow-up period, her body temperature remained within the normal range, and a color Doppler ultrasound of lymph nodes in the neck revealed significant decreases in the sizes of the cervical lymph nodes.