Microbial diversity and antimicrobial resistance from air and manure of layer chicken barns
Bibliographic record
Abstract
Poultry housing environment has vast variety of microbial communities and antimicrobial resistance genes (ARGs), which can be a serious public health concern in addition to their impact on the health of birds. Previous studies conducted elsewhere have demonstrated the metagenomic insights of resistome in poultry farm dust and ARGs against multiple antibiotics were predominantly recorded. Poultry litter and manure are spread in agriculture fields as fertilizer, which may pose a risk to environment and human and animal health. The thesis work was aimed at investigating the microbiome and resistome in air and manure of layer chicken barns across Alberta. Additionally, the host tracking of ARGs and the phenotypic and genotypic antimicrobial resistance profiling of non aureus Staphylococcus species (NASS) were conducted. The sampling was carried out in 15 (cage and floor housed layer chicken) barns across Alberta during 2022-24 and processed the samples by shotgun metagenomics for microbiome and resistome characterization, and whole genome sequencing of isolated bacterial colonies (NASS). Bacillota, Actinomycetota and Pseudomonadota were most relatively abundant phyla in study samples. Analysis of ARGs indicated that resistance was mainly for tetracyclines, aminoglycosides and lacosamide classes of antibiotics. A total of 113 unique ARG subtypes from 19 classes of antimicrobials were identified in air, while 166 unique ARG subtypes were discovered in manure samples. A total of 251 high quality MAGs were extracted from sequences including 249 bacterial and 2 archaeal genomes. Interestingly, 22 bacterial MAGs were not classified to species levels and were potentially the unique and novel taxa. ARGs were mainly harbored by Staphylococcus, Alistepes, Romboutsia, and Enterococcus species. Seven Staphylococcus equorum, 5 Staphylococcus shinii, 1 Staphylococcus pseudoxylosus, 1 Staphylococcus cohnii, and 1 Staphylococcus gallinarum isolates were confirmed and identified by WGS and comparative genomic analysis. This study provides a strong argument for the need for policy change regarding treatment of litter and manure prior to application on agriculture land in Alberta. Presence of potential opportunistic and pathogenic microorganisms and ARGs in poultry barn bioaerosols and litter can be a serious One Health concern.
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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) | 0.001 | 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".