Streptococcus pneumoniae as a Cause of Community-Acquired Pneumonia: Changes Over the Past 100 Years
Bibliographic record
Abstract
In the preantibiotic era, Streptococcus pneumoniae (Sp) was responsible for >90% of community-acquired pneumonia (CAP). Modern studies identify Sp in only 5–14% of CAP in the United States (US) and Canada and 15–35% in Europe. PubMed and Google Scholar were searched for studies reporting the etiologic spectrum of CAP in adults in the US, Canada, or Europe. Inclusion of each study required the use of a conventional case definition for CAP and application of standard microbiologic techniques in >50% of cases. Reports on a single subpopulation (immunocompromised, elderly, etc.) or clinical setting (ICU, outpatient, etc.) were excluded. Thirty-one studies from the US and Canada (21,315 patients) and 41 from Europe (25,183 patients) met inclusion criteria. Included studies were published between 1917 and 2015. In the USA and Canada, the proportion of cases caused by Sp decreased significantly over time (Figure 1A) and was inversely related to the proportion of patients with antibiotic use prior to hospital admission (Pearson’s correlation coefficient -0.76 [95% confidence interval −0.48 to −0.90, P < 0.001]). In the US and Canada, the frequency of Sp has continued to decline during the past 4 decades; in contrast, the frequency of Sp has remained stable in Europe during this time (Figure 1B). The proportion of CAP caused by Sp has declined dramatically in the US and Canada during the past 100 years. The initial decline between 1940 and 1965 may be explained by availability of antibiotics. Potential factors contributing to the continued decline include widespread pneumococcal vaccination and declining rates of smoking. The higher frequency of Sp in Europe may be due to lower vaccination rates in adults and higher rates of smoking. Limitations of the present study include heterogeneity among studies in illness severity, comorbidities, microbiologic testing and prior antibiotic use. Frequency of S. pneumoniae as a cause of community-acquired pneumonia (CAP). A. US and Canada, 1917–2013. B. Comparison between Europe (red) and the US and Canada (blue), 1975–2013. Each circle represents a single study. The area of each circle is proportional to the number of patients in that study. All authors: No reported disclosures.
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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 | 0.012 | 0.032 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.013 | 0.026 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.004 | 0.005 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| 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".