The current standard of care for detection of PJ has significant limitations in COPD patients. There is no reliable in vitro culture system and traditional detection methods are based on histochemical staining with direct fluorescent antibodies (DFA) that target the cyst form of the organism isolated from bronchoalveolar lavage (BAL) fluid. BAL is an invasive diagnostic procedure that often cannot be performed safely in patients with AECOPD due to associated risk of worsening respiratory failure and intubation. In non-HIV patients, PJ is at a lower bioburden and generally exists in the vegetative form rather than the cyst form. The lower PJ cyst burden leads to a lower sensitivity of DFA (20%) which specifically targets the cyst form. This in turn leads to difficulty in identifying PJ in the non-HIV population including transplant and COPD patients. This has led to a lack of clinical trials for potential therapeutic interventions targeting PJ to treat AECOPD or to prevent progression of COPD. A novel method of non-invasive sample collection of sputum analysis with the Unyvero system which is a novel nucleic acid amplification testing (NAAT) based assay demonstrated to have high sensitivity for PJ is being used to determine prevalence of PJ in the AECOPD population. The ability to routinely identify the subgroup of patients colonized with PJ among the hospitalized patients with AECOPD is a necessary step toward selection of the most appropriate potentially treatable patients to include in this pilot study designed to treat AECOPD.

Trimethoprim-sulfamethoxazole (TMP-SMX) is the standard of care for treating PJ pneumonia in HIV patients, and has been shown in prior studies to have high clinical cure rates. Our intervention is adding TMP-SMX to the treatment regimen for patients hospitalized with AECOPD and colonized with PJ. The goal of this study is to determine if treating PJ in AECOPD with confirmed PJ colonization has a beneficial clinical impact. As a secondary goal of the study, it will be determined if TMP-SMX can decolonize these patients and if the decolonization is durable for at least 3 months.

Participants will be randomized in a 1:1 ratio to one of two groups. Group #1 will receive a suspension with the equivalent of one double strength (DS) TMP-SMX by mouth every 12 hours. Group #2 will received a suspension with placebo by mouth every 12 hours. If the participant is discharged prior to completing the 10-day course of the medication, they will be sent home with the remaining days of study medication and a medication diary which will be collected at the end of therapy visit. When a patient with PJ pneumonia is hypoxic, the treatment of the PJ in addition to TMP-SMX includes steroids.

Upon consent patients will be given the COPD Assessment Test (CAT) (https://www.mdcalc.com/copd-assessment-test-cat), a validated scoring system used in COPD patients to assess progression, functional status, and effectiveness of pulmonary rehabilitation. Participants will be monitored daily while in the hospital for highest oxygen need, need for non-invasive or invasive mechanical ventilation, and adverse events, daily monitoring will be carried out by the nurse coordinator. Medications used for the treatment of COPD and antibiotics used will be collected retrospectively for each patient. If the patient remains hospitalized at end of therapy, 30 days, or 90 days then follow up will occur in the hospital. Otherwise, the patient will be asked to come to the Infectious Diseases Clinical Research Office for follow up visits at end of therapy (+0-3 days to allow for schedule issues and end of therapy falling on a weekend), 30 days +/-5 days, and 90 days +/- 10 days. A $30 stipend will be paid to the participants after each follow up visit. At the end of treatment visit, the medication diary will be collected. At each follow up visit, the nurse coordinator will review the patient's need for oxygen, their medications for the treatment of COPD, any need to see a physician or go to an urgent care or an emergency room for COPD, and any admission to the hospital for COPD. The CAT will be administered at each follow up visit. An expectorated sputum sample will be collected at each follow up visit which will be transported to the Infectious Diseases Research Laboratory for analysis; sputum samples will be processed and analyzed with the Unyvero system for presence of PJ by polymerase chain reaction (PCR).