Bibliographic record
Abstract
Streptococcus pneumoniae is a major cause of morbidity and mortality globally, causing respiratory infections, including community-acquired pneumonia and invasive pneumococcal disease (IPD). Antibiotic resistance in S. pneumoniae is a very serious clinical and public health problem worldwide as such infections are among the leading causes of illness and death for young children, people with underlying debilitating medical conditions and elderly people. Several interventions have been made to limit the further emergence and spread of drug-resistant S. pneumoniae, including campaigns for appropriate use of antibiotics and the introduction of pneumococcal conjugate vaccines. But even more effective strategies are needed in the community. In this Supplement to the Journal of Antimicrobial Chemotherapy the most predominant serotypes of invasive S. pneumoniae infection collected by the annual SAVE study in Canada between 2011 and 2015 are characterized. SAVE is an ongoing, annual, national study focused on characterizing invasive isolates of S. pneumoniae obtained across Canada. During the survey period, it was found that the overall rate of MDR S. pneumoniae was 6.2%. The susceptibility of invasive isolates of S. pneumoniae in Canada has significantly increased to penicillin, clindamycin and ceftriaxone, although there was a significant decrease in MDR phenotypes. PCV-13 vaccine included the most commonly identified serotype 19A, but other increasingly important MDR serotypes in the present study, such as 15A, 24F and 33F, are not included in the current vaccines. Additionally, the observations made indicate the high genetic variability of S. pneumoniae major serotypes. Molecular and phylogenetic analyses identified serotypes 19A, 15A, 6C, 9N and 33F as highly diverse, whereas 7F, 22F and 11A demonstrated clonality. The pathogen has also demonstrated the capacity to propagate successful clones, such as ST320, ST433 and ST191, while also participating in frequent recombination to increase genetic diversity and spread antimicrobial resistance genes. Thus, despite successful use of conjugate vaccines, S. pneumoniae was found to remain a highly diverse organism in Canada. Last but not least in this Supplement, the increased ability of WGS to discriminate between closely related isolates has been illustrated. Considering the fact that S. pneumoniae continues to evolve in Canada, WGS will be a valuable tool for epidemiological and antimicrobial resistance studies. None to declare.
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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 | 0.001 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.601 | 0.413 |
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".