A 49-year-old man reported to the emergency room (ER) on March 16, 2021, with one month of shortness of breath, productive cough, and fever, as well as a nine-kilogram weight loss. He had mild COVID19 pneumonia three months before admission. His temperature was 38.1 oC, blood pressure 101/52, pulse rate 108 beats per minute, respiratory rate 20 breaths per minute, and ambient air oxygen saturation 99%. He looked malnourished and pail, he had finger clubbing. The right lung had fine crepitations, and the submandibular and cervical lymph nodes were palpable but not painful. Table (1) shows his initial lab tests. A chest radiograph showed a right sided homogenous infiltration with a cavitary lesion at the same site as shown in Fig. (1).The patient was admitted with pneumonia and has been given piperacillin-tazobactam 4.5gm every 6 h and azithromycin 500 mg once daily empirically. SARS-CoV-2 PCR was positive; sputum culture revealed susceptible pseudomonas aeruginosa; ceftazidime 2gm every 8 h replaced piperacillin-tazobactam.

Image (i) A chest radiograph upon arrival of the first admission, demonstrates a right lower zone infiltration with a small cavitary lesion. Image (ii) CT chest of the first admission, demonstrate a 2.7 × 3 cm heterogenous enhancing soft tissue lesion compressing the right lower lobe segmental bronchus (red arrows). Image (iii) CT Chest of the second admission, show the evolving right lower lobe mass reaching 10.3 × 10.5 cm making more compression on the right lower segmental main bronchus (green arrows) with the presence of air pockets as demonstrated as shown in images

As a result of elevated liver function tests, abdominal ultrasonography was performed, which revealed diffuse hepatic steatosis. Human immunodeficiency virus (HIV) antibody test was done that turned to be positive.In addition to primary sclerosing cholangitis caused by Epstein-Barr virus (EBV) versus cytomegalovirus (CMV), mycobacterial infections were suspected. The patient’s CD4 count was 20 cells/cu mm, while the CMV and EBV viral loads were 659,072 and 81 IU/mL, respectively. HIV viral load and genotypic analysis were unavailable at the time. Negative results have been reported for the syphilis, hepatitis C virus serology, and hepatitis B surface antigen. Magnetic resonance cholangiopancreatography was done that showed no intra or extra hepatic biliary obstruction in addition to a 0.5 × 0.5 cm lesion in segment 7 in keeping with haemangioma.

As verified by the ophthalmology team, the patient lacked clinical evidence of CMV retinitis, and he was started on valganciclovir 900 mg twice daily in addition to Co-trimoxazole 1 double strength three times per week as prophylaxis. As shown in Fig. (1), a computed tomography (CT) off the chest revealed a 2 by 3 cm mass in the right lower lobe at the right main bronchus with ground glass opacity and collapse. The patients underwent bronchoalveolar lavage (BAL) without a biopsy. The procedure revealed a 2 by 3 cm polyp in the right bronchus. In addition to cytology and mycobacterium tests, BAL samples were sent for bacterial and fungal culture. The results are listed in Table (2). The patient went home on valganciclovir, Co-trimoxazole as prophylaxis and ciprofloxacin 750 mg twice daily until review his pending laboratory results at the virology outpatient clinic.

On the basis of clinical presentation and two positive acid-fast bacilli samples with negative TB PCR, the patient was diagnosed with nontuberculous mycobacterium infection at the virology clinic on 11 April 2021. As a result, ethambutol 1.2 g once daily, clarithromycin 500 mg twice daily, and rifampicin 600 mg once daily were added to valganciclovir 900 mg twice daily, Co-trimoxazole 960 mg three times weekly, and ciprofloxacin 750 mg twice daily. The patient was given a three-week follow-up appointment and advised to repeat sputum for acid-fast bacilli, liver function test, computed tomography of the chest, and CMV viral load. The patient missed his appointment and showed up on May 30, 2021. On that visit, his symptoms did not improve; however, he had trouble being adherent with his medication. While ciprofloxacin was discontinued, he was instructed to continue taking valganciclovir, Co-trimoxazole, ethambutol, clarithromycin, and rifampicin.On June 13, 2021, he returned to the clinic with progressive weight loss and cough as he struggled to adhere to his medication. Genvoya (Elvitegravir 150 mg, cobicistat 150 mg, emtricitabine 200 mg, tenofovir alafenamide 10 mg) was prescribed, and the patient was instructed to adhere to his medication. HIV viral load, CMV viral load, lymphocyte analysis, and computed tomography of the chest and abdomen were requested.

On June 21, 2021,the patient presented to the ER with complaints of progressive fatigue, poor appetite, fever, generalized body pain, and congestion, as well as poor medication adherence.He reported that he wasn’t taking Genvoya and was not compliant with all medications. Examination showed a severely cachectic man with severe pallor. The preliminary investigations are outlined in Table (1). Meropenem 1 gm every 8 h and ganciclovir 250 mg twice daily were added to Co-trimoxazole prophylaxis, while other medications were discontinued. Despite inadequate medication adherence, the CMV viral load decreased to 1,592 IU/mL from 659,072 IU/mL in March 2021, and the HIV viral load was 3,541 IU/mL.

Due to severe anaemia, packed red blood cells were given. The patient underwent upper and lower gastrointestinal (GI) endoscopies. The upper GI scope revealed only mild gastritis, whereas the lower GI scope revealed extensive ulcers, nodules, and erythematous changes involving the right colon. As a result, several samples were taken from the right and left sides of the colon for full analysis. In Fig. (2), images of lower GI endoscopy are showed.

Gross endoscopic appearance of the right colon showing the cecal base at ileocecal valve with deformed looking. Multiple ulcers ranging between 5 mm and 1 cm in diameter with noticed with raised edges and whitish base. Some ulcers were oozing blood and others were covered by clots

CT of the chest and abdomen revealed a progression of right lower lobe mass and worsening lung parenchymal disease with bilateral effusion and a small pericardial effusion, as depicted in Fig. (1). The expanding right lung mass was biopsied using ultrasound guidance, and samples were sent for microbiology and histology evaluation. TB culture from the lung mass was pending at the time, while PCR and three acid-fast bacilli smears came back negative. Candida krusei was isolated from the lung mass, so voriconazole treatment was initiated. As shown in Fig. (3), the right colon histological sample demonstrated malakoplakia with positive CMV stains while lung showed malakoplakia only.

(1) Malakoplakia. High magnification view showing epithelioid histiocytes with abundant eosinophilic cytoplasm and intracytoplasmic round basophilic targetoid inclusions (Michaelis-Gutmann bodies) (arrows), diagnostic of malakoplakia(Lung). (2) Malakoplakia. High magnification view showing colonic epithelium with underlying epithelioid histiocytes (arrow) with abundant eosinophilic cytoplasm(Colon). (3) The Michaelis-Gutmann bodies are highlighted with a von Kossa stain. (4) Immunostaining for CMV is POSITIVE

Ascorbic acid was added to the patient’s medication. He improved clinically and requested discharge. Before discharge, ganciclovir was replaced with valganciclovir, co-trimoxazole continued three times per week, and voriconazole continued 200 mg twice day with ascorbic acid. Descovy (emtricitabine and tenofovir) and Dolutegravir were also given. He tolerated his medicines well and discharged home with two weeks follow up in virology clinic.

10 days later, patient returned to ER with worsening shortness of breath, poor oral intake, and acute renal injury. He was unstable and started double inotropic support. SARS-CoV-2 was isolated again. The right lung biopsy sample from the previous admission showed malakoplakia with Rhodococcus equi positive culture. The patient received broad-spectrum antimicrobials. After three days, the patient passed away he developed acute respiratory distress syndrome, multi-organ failure, and severe coagulopathy.