The use of E. coli phylogrouping and microbial source tracking (non-species specific, human-specific, bovine-specific bacteroidales markers) to elucidate hydro(geo)logical contamination mechanisms in southeastern Ontario, Canada
Bibliographic record
Abstract
In Ontario, monitoring, maintenance, and treatment of private drinking systems (e.g. wells) are the responsibility of the well owner. Fecal contamination of drinking water threatens public health, particularly in rural communities which are often fully reliant on unregulated private groundwater as a primary drinking water source. Private well users face a higher risk of acute gastrointestinal illness compared to those served by municipally operated systems (Murphy et al., 2016). Accordingly, the current study sought to characterize the fecal indicator, E. coli , isolated from southeastern Ontario private groundwater wells, including phylogroups and host source. Results were examined in the context of antecedent climate and local hydrogeological setting to elucidate likely contaminant sources and pathways. A total of 737 E. coli isolates from 260 private wells were assigned to phylogroups using the Clermont PCR phylotyping method, with likely host source determined using host-specific Bacteroidales 16S rRNA RT qPCR assays. Multivariate models were developed for the main E. coli phylogroups (A, B1, B2, and D) and all microbial source tracking markers. Models were coupled for interpretation where possible, based on associations between phylogroups and MST markers. Preferential subsurface flow, and to a lesser degree, overland flow, were likely mechanisms of contamination across all models. Distinct temporal associations were found based on the fecal source. Multiple models were developed and will be discussed, in an attempt to elucidate source-specific contamination mechanisms, in support of risk assessment and appropriate protective actions. • Collected 737 E. coli isolates from 260 private wells over two years. • Multivariate models of contamination using E. coli phylogroup and MST markers. • Distinct temporal associations found based on fecal source. • Preferential subsurface flow a likely contamination mechanism across all models. • Concurrent model suggests multiple simultaneous contamination mechanisms.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 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".