| broad-scale environmental context | poultry |
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| collection date | 2019-10 |
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| environmental medium | poultry litter |
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| geographic location | Italy |
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| investigation type | metagenome-assembled genome |
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| isolation source | chicken gut metagenome |
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| project name | Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment – in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms. |
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| sample name | ERR11768915_binner123_Refined_11 |
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| ENA first public | 2024-11-29 |
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| ENA-CHECKLIST | ERC000047 |
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| INSDC center name | EMG |
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| INSDC status | public |
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| Submitter Id | ERR11768915_binner123_Refined_11 |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
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| assembly software | MetaSPAdes_v3.15.5 |
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| binning parameters | default |
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| binning software | MGnify-genomes-generation-pipeline_v1.0.0 |
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| broker name | EBI-EMG |
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| completeness score | 96.74 |
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| completeness software | CheckM2_v1.0.1 |
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| contamination score | 1.53 |
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| geographic location (latitude) | missing: third party data |
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| geographic location (longitude) | missing: third party data |
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| local environmental context | chicken |
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| metagenomic source | chicken gut metagenome |
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| sample derived from | SAMEA113907160 |
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| scientific_name | uncultured Eisenbergiella sp. |
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| sequencing method | NextSeq 500 |
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| taxonomic identity marker | multi-marker approach |
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