The impact of pneumococcal vaccination and nasopharyngeal colonization on the performance of a serotype-specific urine antigen detection (SSUAD) assay
Bibliographic record
Abstract
To better inform pneumococcal immunization policies, ongoing surveillance for pneumococcal community-acquired pneumonia (CAP) is crucial. To estimate the serotype-specific CAP burden of pneumococcal disease following the introduction of a new 15-valent pneumococcal conjugate vaccine (PCV), V114, a 15-plex serotype-specific urine antigen detection (SSUAD) assay was developed as a tool for surveillance of Streptococcuspneumoniae serotypes. V114-017 (NCT03547167; EudraCT 2017-004915-38) was a phase 3 randomized controlled trial in which participants (18-49 years) received V114 or 13-valent PCV (PCV13; as an active comparator), followed 6 months later by 23-valent pneumococcal polysaccharide vaccine (PPSV23). Here, we report findings from a prespecified sub-study nested within the phase 3 trial that descriptively assessed the impact of nasopharyngeal/oropharyngeal (NP/OP) carriage and pneumococcal vaccination on serotype detection with the SSUAD assay. In total, 301 individuals (all American Indian/Alaska Native) participated in the sub-study. NP/OP and urine samples were collected at 10 timepoints between baseline (prior to vaccination) and Month 7 (30 days following vaccination with PPSV23). NP/OP carriage was determined using qualitative polymerase chain reaction for pneumococcus detection and serotyping, and urine samples were tested in parallel with SSUAD. At any timepoint, NP/OP carriage was <2.0 % for 10 of the V114 serotypes; carriage was ∼2.6 % for serotype 1 and ranged between 4.0 % and 7.0 % for serotypes 4, 5, 9V, and 33F. At baseline, serotype-specific pneumococcal polysaccharide antigens were detected by SSUAD in only six study participants for serotypes 19A, 19F, and 1. SSUAD positivity for serotypes 4, 5, and 9V increased transiently following vaccination with V114/PCV13 and PPSV23, while SSUAD positivity lasted the longest for serotype 19A following PPSV23 vaccination. In general, SSUAD positivity appeared unrelated to NP/OP carriage. Our findings suggest SSUAD can support pneumococcal disease surveillance and vaccine effectiveness research, excluding individuals with recent pneumococcal vaccination to avoid false-positives.
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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 | 0.010 | 0.015 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".