Unexpected High Frequency of <i>Pneumocystis jirovecii</i> Pneumonia at SCID Diagnosis
Bibliographic record
Abstract
Patients with severe combined immunodeficiency (SCID) have a predisposition to opportunistic infections, including Pneumocystis jirovecii. Previous reports based on traditional microscopy and culture estimate the prevalence of Pneumocystis jirovecii pneumonia (PJP) at diagnosis of SCID around 20%. Polymerase chain reaction (PCR) for the diagnosis of PJP in bronchoalveolar lavage (BAL) demonstrates high sensitivity when compared to traditional culture methods. We present three cases of SCID who underwent routinely Pneumocystis jirovecii PCR at the time of SCID diagnosis in the past year, during which PCR testing for Pneumocystis jirovecii became routinely available at our institution. All patients underwent a chest computed tomography (CT) at the time of diagnosis. Imaging findings included ground-glass opacities in two patients, consolidation in two patients, and atelectasis in two patients. One patient had no respiratory symptoms, oxygen requirement, or clinical evidence of pulmonary involvement prior to the CT scan. However, imaging revealed ground-glass opacities and consolidation. During the BAL procedure, the patient experienced clinical deterioration, including a respiratory arrest, and required mechanical ventilation. All three SCID patients tested positive for Pneumocystis jirovecii by PCR at the time of diagnosis. Each received empirical treatment with co-trimoxazole prior to the availability of PCR results. Only qualitative PCR was available, which may lead to some false-positive results. However, in the context of SCID patients with consistent clinical or radiological findings, infection was presumed. With the advent of more sensitive and specific diagnostic tools such as PCR for Pneumocystis jirovecii, the true incidence of this infection at the time of SCID diagnosis may be higher than previously recognized, even among asymptomatic patients. We recommend routine PCR-based screening for Pneumocystis jirovecii in all newly diagnosed SCID patients, when available.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.003 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".