Wastewater-based surveillance of Bordetella pertussis during an outbreak in Alberta, Canada
Bibliographic record
Abstract
Background: Whooping cough, caused by Bordetella pertussis (BP), is a vaccine-preventable illness spread through respiratory droplets. As the disease disproportionally impacts infants and children, vaccination is part of the routine childhood series in Canada. However, vaccine hesitancy and resultant declining rates of community immunity increase the risk of disease. We leveraged our existing wastewater-based surveillance (WBS) network to assess its ability to track clinical disease in response to an outbreak in southern Alberta. Methods: For seven months before and after the declaration of a January 2023 outbreak, wastewater samples were collected at approximately weekly intervals from five municipalities in southern Alberta (~1.05 million residents). 24-hour composite wastewater was pelleted, mechanically lysed, and DNA extracted. B. pertussis gene BP283 was quantified by qPCR and normalized against total-bacterial 16s rRNA. De-identified clinical data was obtained from Alberta Health Services (AHS) and vaccination rates collected from the AHS Interactive Health Data Application dashboard ( http://www.ahw.gov.ab.ca/IHDA_Retrieval/ ). Per local guidelines, cases could be diagnosed through molecular testing, or if an individual had a strong epidemiological link to a known case and compatible whooping cough symptoms ( https://open.alberta.ca/publications/pertussis ). Cases were mapped to sewershed areas using forward sortation areas. Fishers exact test was used to determine the association of the categorical variables of positive wastewater samples and clinical cases diagnosed in the week following, as well as to compare rates of wastewater positivity before and after the outbreak was declared. Results: Over the study period 296 cases of whooping cough were identified, with 256 after the outbreak was declared. No wastewater samples were positive for BP prior to the outbreak (0%) and 22 were positive during the outbreak (19.8%), p = 0.0006 (Figure 1). Of the positives, the median ratio of BP:16s rRNA was 8.89x10-9 (IQR: 5.31x10-9 to 4.19x10-8). Detection of BP in the wastewater did not necessarily predict the occurrence of cases the following week within individual municipalities, but there was an association when all sites were aggregated (OR 2.47 [CI: 1.01–6.05], p = 0.04). Vaccination rates in the communities ranged from 40.9% to 72.2%, and did not associate with wastewater detected Bordetella pertussis. Conclusion: BP can be detected in wastewater during outbreak periods, though infrequently and in very low concentrations. For WBS to be used as an effective tool to monitor and potentially mitigate cases of whooping cough for WBS (and other respiratory pathogens which are not readily amplified in the gastrointestinal tract), assay sensitivity will need to be improved.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".