A 52-year-old man was admitted to our hospital with recurrent episodes of urinary urgency, frequency and painful urination with elevated blood creatinine for 18 months. The patient had a history of systemic lupus erythematosus and lupus nephritis for 14 years. He was routinely treated with "prednisone 10 mg/d, leflunomide 20 mg/d, and hydroxychloroquine 0.4 g/d". The patient first developed urinary frequency and urgency in 2013, and routine urine tests suggested the presence of white blood cells, which improved with anti-infective treatment. Frequent, urgent and painful urination reappeared in 2019 and anti-infective treatment was given with poor results. The patient's symptoms persisted and several repeat urine tests showed leukocytes, but urine cultures were not abnormal. The renal function was reviewed on 13 January 2021 for abnormalities and elevated blood creatinine, and herbal treatment was given.
On July 11, 2022, he was admitted to our nephrology department for treatment. A routine urine examination showed 434.1/muL white blood cells, 53.7/muL red blood cells and 64.9/muL bacteria (Figure 1). Blood sedimentation 44 mm/h; C-reactive protein 16.82 mg/L; no abnormalities in routine blood (Table 1); renal function: creatinine 124 mumol/L, urea 8.58 mmol/L; no abnormalities in urine culture. Anti-nuclear antibody +1:320; anti-dsDNA antibody 131.1 IU/mL. Urological ultrasound: right kidney stone, left hydronephrosis and left ureteral dilatation. Computed Tomography (CT) of kidneys and bladder: 1. Stones in both kidneys; 2. Thickening of the left posterior wall of the bladder with hydronephrosis of the left kidney and dilated effusion of the left ureter; 3. Cyst in the right kidney (Figure 2). We considered complicated urinary tract infections, interstitial cystitis, and poor anti-infective effect. On day 18 of admission, urethral stricture dilatation, transurethral suburethral cystoscopy, hydrodistension and cystocentesis biopsy were performed. Pathology showed a microscopic examination of transverse muscle and a little fibrous and fatty tissue. On the 24th day of admission, the urine test was repeated: white blood cells 951.3/muL, red blood cells 1258.8/muL and bacterial count 274.7/muL. The patient requested to be discharged after his condition was more stable than before.  
On 16 August 2022, the patient was readmitted to the hospital with "increased urinary frequency, urgency and hematuria of the naked eye one week after surgery". The patient had an elevated body temperature of 38.8 C. And We found him to be unresponsive when we talked to him. Blood count: white blood cells 10.22*10^9/L, red blood cells 4.36*10^12/L, platelets 203*10^9/L; Urine routine: leucocytes 2618.50/muL, bacterial count 2937.7/muL and a large number of red blood cells. Renal function: creatinine 121.0 mumol/L, urea 5.64 mmol/L. We gave bladder irrigation and piperacillin sodium tazobactam anti-infective treatment.
Sudden onset of unconsciousness on the 3rd day of admission, and cranial magnetic resonance imaging (MRI) of the brain showed: 1. ventral diffusion-weighted imaging (DWI) punctate high signal in the pontine brain; 2. bilateral frontal lobes with a little lacunar cerebral infarction; 3. mild demyelination changes in the white matter of the brain around the ventricles bilaterally; 4. mild septal sinusitis; 5. right vertebral artery terminal stenosis, right posterior cerebral artery P3 segment, anterior cerebral artery local mild stenosis, cerebrovascular atherosclerotic changes (Figure 3). We considered excluding the possibility of cerebral hemorrhage and cerebral infarction. And no meningeal enhancement changes were seen. The patient had a recurrent elevated temperature and was unconscious. We, therefore, concluded that lupus encephalopathy could not be ruled out and added methylprednisolone 40 mg/d. The symptoms did not improve significantly and there were still recurrent fevers and occasional headaches. 
A repeat cranial MRI on the 9th day of admission showed no specific abnormalities and an initial pressure of 125 mmH2O was measured by parallel lumbar puncture. Cerebrospinal fluid laboratory results indicated: lactate dehydrogenase 71 U/L, glucose 1.22 mmol/L, chloride 113.2 mmol/L, adenosine dehydrogenase 4.8 U/L, protein 1.660 g/L, cell count 110*10^6/L, immunoglobulin G 216.0 mg/L, immunoglobulin M 4.5 mg/L, immunoglobulin A 94.4 mg/L (Table 2). No antacid bacilli were detected in the cerebrospinal fluid concentrate collection test. The cerebrospinal fluid culture was not abnormal. The cerebrospinal fluid antibody test for Mycobacterium tuberculosis was negative. Cerebrospinal fluid DNA quantification of Mycobacterium tuberculosis was negative. Cerebrospinal fluid fungal microscopy was unremarkable. Multiple blood cultures were unremarkable. We then discussed with the family about sending the cerebrospinal fluid out for mNGS.
Day 13 mNGS results showed Mycobacterium tuberculosis complex sequence number 3358 in the cerebrospinal fluid. At this point, the patient's diagnosis of tuberculous meningitis was clarified. Meanwhile, we applied the Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K) to score the patient's current disease activity and the result was a score of 2. The SLE disease was largely inactive. He was transferred to the Infectious Diseases Hospital on 28 August 2022 for continued treatment. Mycobacterium tuberculosis was found in the urine concentrated collector antacid test on 4 September and was treated with isoniazid, rifampicin, ethambutol and pyrazinamide against tuberculosis. At the six-month follow-up, the patient is still on continuous anti-tuberculosis treatment and is in stable condition.