Metagenomic analysis reveals differences in antibiotic resistance and transmission risks across various poultry...

As living standards in rural areas continue to improve, farmers are increasingly seeking to diversify their farming models beyond monoculture farming. However, the differences in bacterial resistance and the associated transmission risks between monoculture poultry farming and integrated poultry farming remain poorly understood. This study utilizes metagenomic methods to examine the distribution and transmission of antibiotic resistance across three types of farms in Zhejiang Province, as well as to investigate the horizontal transmission mechanisms of plasmid-mediated bla_NDM within these agricultural systems. An analysis of 26 environmental samples and 12 saliva samples from six poultry farms with different models has revealed that integrated poultry farms exhibit a more complex microbial composition and more severe resistance compared to monoculture farms. Furthermore, a bla_NDM positive plasmid pndm-CD with complex conjugation transfer region was found in the integrated farms. The insertion sequence (IS) ISCR1 present in the upstream of bla_NDM has the potential to promote its spread, while the downstream complex structure IS26-bla_CTX-M-IS2-qnrB-TinR-ΔISKrA14 enhances the resistance of the host to β-lactam antibiotics, and improves the competition potential of the host bacteria in the anti-antibiotic environment. This research offers the first metagenomic analysis of the differences in bacterial resistance and transmission risks between various poultry farming models. These results offer a solid theoretical basis for managing the spread of antibiotic resistance in mixed chicken and duck farming operations. Additionally, they are significant for ensuring the health of agricultural workers and the hygiene safety of the poultry meat supply chain.