A 37-year-old South Asian male was admitted to our hospital with dysuria and urine retention for one day. He has a history of stage 3 chronic kidney disease and bilateral obstructive uropathy due to kidney stones which required multiple invasive urological interventions three months ago prior to this presentation. Additionally, he was diagnosed with painful bladder syndrome requiring regular intravesical injections; the last one was four weeks before this presentation. On the following day of admission, he developed fever (temperature of 38.7  C), and the laboratory investigations revealed white blood cells (WBC) of 7.1 x 103/uL (normal range:4-10), C-reactive protein (CRP) of 93.7 mg/L(elevated), creatinine of 179 umol/L (within his baseline range), and urine WBC of 242/ hpf. Blood and urine cultures were negative. The urinary tract computed tomography revealed bilateral hydroureteronephrosis with no detectable ureteric or bladder stones (Fig. 1). Despite being on ertapenem (accordingly to his previous culture and sensitivity) for more than three days, he still had worsening urinary symptoms and spiking temperature. Repeated urine analysis revealed the presence of pus cells with negative cultures again. Accordingly, given the presence of recurrent sterile pyuria and his history of extensive urological interventions, a work-up for a mycobacterial UTI was performed. The Acid-Fast Bacilli (AFB) smears of the urine sample were negative. Cystoscopy with bladder biopsy was done, which revealed non-necrotizing granulomatous cystitis (Fig. 2). Two weeks later, urine culture(MTB cultures using both solid media, Middlebrook 7H11, and liquid media using BACTEC MGIT 960) grew Mycobacterium abscessus complex (MABC), which is later identified through real time PCR as Mycobacterium abscessus subspecies abscessus.
Subsequently, the patient was commenced empirically on a combination of meropenem (1 gm every 12 h), amikacin (433 mg once daily), ciprofloxacin (400 mg intravenous every 8 h), and clarithromycin (500 mg orally every 12 h). However, his creatinine worsened (increased from 170 to 249) due to amikacin nephrotoxicity; hence, amikacin was replaced by intravenous linezolid (600 mg every 12 h). However, two weeks after starting linezolid, the patient developed significant thrombocytopenia (platelet count dropped to 54), and subsequently, linezolid was substituted with doxycycline (100 mg oral every 12 h). The final urine culture and drugs susceptibility showed that the organism is resistant to doxycycline and ciprofloxacin and sensitive to tigecycline and clofazimine (Table 1). Therefore, he was kept on meropenem, tigecycline, clofazimine, and clarithromycin for two months, then meropenem and tigecycline stopped, and he was continued on clofazimine and clarithromycin. His monthly repeated urine mycobacterial cultures showed no growth, his HIV test was negative, and no abnormalities were detected in the chest- X-ray. At eight months follow-up from starting treatment, the patient was afebrile and asymptomatic, tolerating oral clofazimine and clarithromycin with persistent negative urine culture for mycobacterium abscessus. He was planned for 12 months of therapy from the first negative urine cultures.