386 Decoding poultry threats: Unveiling sequencing types, serogroups, and antimicrobial resistance of avian pathogenic Escherichia coli in Alberta, Canada.
Bibliographic record
Abstract
Abstract Background: Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, leading to substantial economic losses in Canada and other regions. Avian fecal E. coli (AFEC) is considered a potential reservoir for APEC, due to shared genetic characteristics. Hypothesis: Avian Pathogenic Escherichia coli (APEC) isolates from poultry in Alberta have distinct phenotypic and genotypic profiles, characterized by variations in virulence factors, antimicrobial resistance genes, and phylogenetic relatedness, which may contribute to differences in pathogenicity and adaptability to specific host and environmental conditions. Objective: This study aimed to identify and profile phenotypic and genotypic characteristics of potential pathogenic E. coli that cause poultry colibacillosis in Alberta. Methods and Results: A total of 100 APEC isolates from diseased and dead chickens (broilers and layers) and turkeys from 45 farms collected between 2021 and 2023 were subjected to serogroup typing, APEC-associated virulence gene (VG) profiling, antimicrobial susceptibility testing, whole genome sequencing, multilocus sequence typing, and phylogenetic analysis. Additionally, 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. A phylogenetic tree of 100 APEC isolates and 89 AFEC isolates was also constructed. We identified 27 serogroups, 38 known and 2 novel sequence types (STs), and varied VG distribution across APEC isolates from chickens and turkeys. Interestingly, there were variations in VG among AFEC strains 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 multiple fecal isolates that shared identical ST and serotypes with APEC strains. This study is the first to document characteristics of APEC and poAPEC isolates that cause or potentially cause colibacillosis morbidity and mortality in chickens and turkeys in Alberta. A phylogenetic tree of 20 APEC isolates from Québec with representative AFEC, APEC and pAPEC was also constructed, indicating genetic relatedness with APEC, AFEC and poAPEC. Conclusions: Various APEC phenotypes and genotypes can lead to colibacillosis in poultry, including layers and may originate from commensal E. coli present 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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| 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) | 0.001 | 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".