Exploring the molecular epidemiology of blaCTX-M mediated resistance among Enterobacterales from Canadian domestic animals
Bibliographic record
Abstract
Historically, extended spectrum cephalosporin (ESC) resistance among Enterobacterales in Canada has been attributed to the blaSHV and blaCMY gene families. However, this pattern is beginning to change with the emergence of the blaCTX-M among bacteria since the early 2000’s. It has been demonstrated that food animals can act as a reservoir for ESC resistance. Since the microbiota of humans, animals and the environment are interconnected, it’s important that practices are implemented to limit the production of resistance. Understanding how mobile genetic elements carrying these resistance determinants influence bacterial persistence could be an important factor in informing these practices. Therefore, the objectives of this thesis were twofold. First being to identify and evaluate major reservoirs of ESC resistance among Canadian domestic animals and assess their similarities with regards to their associated resistance determinants. Second, to evaluate how blaCTX-M and its associated mobile genetic elements behave in comparison to commonly recovered ESC resistance genes circulating in Canada (i.e., blaCMY-2). To meet these objectives, we used short-and long-read genome sequencing to characterize blaCTXM-carrying Escherichia coli isolates and plasmids from Canadian domestic animals (i.e., poultry, swine, cattle, horses, and dogs). In vivo experiments were then performed to assess the impact of widespread IncI1/ST3/CTX-M-1 and IncI1/ST12/CMY-2 plasmids on the persistence of Salmonella Heidelberg in chickens. Not unlike what has been reported globally, the most widely recovered blaCTX-M variants from Canadian domestic animals included blaCTX-M-1,14,15 -27 and -55. The spectrum and prevalence of these variants differed between animal species and is likely related to the number and types of transmission routes feeding into the farm. Along with the identification of conserved plasmids (i.e., IncI1/ST3 and IncHI1/ST2) circulating within and between animal species, clonal spread of some E. coli STs was also apparent. Thus, highlighting the important role that both horizontal gene transfer and clonal spread play in the transmission of blaCTX-M. In vivo experiments showed that IncI1/ST3/CTX-M-1 aids in persistence over time in comparison to IncI1/ST12/CMY-2, however neither plasmid provided a significant fitness advantage. Further work is necessary to identify the factors contributing to the success of IncI1/ST3/CTX-M-1 (e.g., enhanced gut colonization and conjugation assisted persistence).
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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".