Aetiology of Lobar Pneumonia Determined by Multiplex Molecular Analyses of Lung and Pleural Aspirate Specimens in The Gambia
Bibliographic record
Abstract
Abstract Background Pneumonia aetiology generally relies on insensitive blood cultures or an assumption that organisms in the pharynx are causal. We determined the causes of lobar pneumonia in rural Gambia using lung aspiration. Methods Pneumonia surveillance was undertaken among all ages. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected patients. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in August 2009 and replaced by PCV13 from May 2011. We used conventional microbiology, and from April 8, 2011 to July 17, 2012, utilized a multiplex PCR assay on lung aspirates. We calculated proportions with pathogens, associations between co-infecting pathogens, and PCV effectiveness. Results 2,550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed multiplex PCR on 156 lung and 4 pleural aspirates. Pathogens were detected in 116 specimens, Streptococcus pneumoniae (n=68), Staphylococcus aureus (n=26), and Haemophilus influenzae type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Co-infections were frequent (n=55). M. catarrhalis was detected in eight patients and in every case there was co-infection with S. pneumoniae. The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared to zero doses of PCV was 0.17 (95% CI 0.06, 0.51). Conclusions Lobar pneumonia in rural Gambia was caused primarily by bacteria, particularly S. pneumoniae and S. aureus . Co-infection was common and M. catarrhalis always co-infected with S. pneumoniae . PCV was highly efficacious against vaccine-type pneumococcal pneumonia. Key Messages What is the key question? Using specimens directly from the infected lung, what is the aetiology of lobar pneumonia in rural West Africa? What is the bottom line? Using specimens directly from the infected lung, Streptococcus pneumoniae and Staphylococcus aureus were the predominant causes of lobar pneumonia in rural West Africa and pneumococcal conjugate vaccine effectively prevented pneumococcal pneumonia. Why read on? Learn about the certain aetiology of lobar pneumonia in 160 Gambian patients with specimens directly from the lung.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| 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".