Microbiological and Molecular Identification and Characterization of Avian Pathogenic Escherichia coli from Poultry Farms, Alberta
Bibliographic record
Abstract
Avian pathogenic Escherichia coli (APEC) is the etiological agent of avian colibacillosis, leading to significant economic losses in Canada and elsewhere. Avian fecal E. coli (AFEC) is considered to serve as a potential reservoir for APEC given shared genetic features. This study aimed to profile phenotypic and genotypic features of causative APEC in Alberta. Here, 100 APEC isolates from diseased and dead chickens (broiler and layer) and turkeys from 45 farms collected between 2021 and 2023 were subjected to serogroup typing, APEC-associated virulence gene (VG) profiling, antimicrobial susceptibility testing, multilocus sequence typing, and phylogenetic analysis. In addition, 121 AFEC isolates from five layer flocks were collected to investigate APEC-associated VG carriage in healthy birds. Furthermore, genetic similarity between 22 AFEC strains identified as potential APEC (poAPEC) and APEC strains was assessed through phylogenetic analysis. We identified 27 serogroups, 38 known and two novel sequence types (STs), and varied VG distribution across APEC isolates from chickens and turkeys. Interestingly, variations in VG among AFEC strains were found across distinct egg laying stages or housing systems. Antimicrobial resistance (AMR) genes, especially extended-spectrum beta-lactamase genes were detected in APEC and poAPEC strains across all poultry species. Moreover, phylogenetic analysis revealed close clonal relationships among APEC and poAPEC strains. Notably, we identified a poAPEC isolate that shared ST155 and VGs with an APEC strain. This study is the first to report the characteristics of APEC and poAPEC isolates that cause or potentially cause colibacillosis morbidity and mortalities in chickens and turkeys in Alberta. A variety of APEC phenotypes and genotypes can lead to colibacillosis in poultry farms and may originate from the commensal E. coli found in the gastrointestinal tract of birds.
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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 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 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".