Animal manure is an important source of antibiotics and antibiotic resistance genes (ARGs) in the environment. However, the difference of antibiotic residues and ARG profiles in layer and broiler manure as well as their compost remains unexplored. In this study, we investigated the profiles of twelve antibiotics, seventeen ARGs, and class 1 integrase gene (intI1) in layer and broiler manure, and the corresponding compost at large-scale. Compared with layer manure, broiler manure exhibited approximately six times more residual tetracyclines, especially chlortetracycline. The relative abundances of qnrS and ermA genes in broiler manure were significantly higher than those in layer manure. The concentration of tetracyclines not only had a significantly positive correlation with tetracycline resistance genes (tetA and tetC) but was also positively correlated with quinolone resistance (qepA, qnrB, and qnrS) and macrolide resistance (ermA and ermT). Most ARGs in manure were reduced after composting. However, the relative abundance of sulfonamide resistance gene sul1 increased up to 2.41% after composting, which was significantly higher than that of broiler (0.41%) and layer (0.62%) manure. The associated bacterial community was characterized by high-throughput 16S rRNA gene sequencing. The relative abundances of thermophilic bacteria had significant positive correlations with the abundance of sul1 in compost. The composting has a significant impact on the ARG-associated gut microbes in poultry manure. Variation partitioning analysis indicated that the change of bacterial community compositions and antibiotics contributed partially to the shift in ARG profiles. The results indicate that at industry-scale production broiler manure had more antibiotics and ARGs than layer manure did, and composting decreased most ARG abundances in poultry manure except for sulfonamide resistance genes.
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•Bacterial concentrations from eight stages were 104–105copies/m3.•Diameter influenced clustering of bacterial and HPB lineages.•Dg of 8 HPB ranged from 2.42 to 5.09 μm in composting areas.•Dg of 8 HPB ranged from 3.70 to 8.96 μm in packaging areas.•HPB had high concentrations and small sizes in composting areas. Composting plants are regarded as one of the important sources of environmental bioaerosols. However, limitations in the size distribution of airborne bacteria have prevented our comprehensive understanding of their risk to human health and their dispersal behavior. In this study, different sizes of airborne bacteria were collected using an eight-stage impactor from a full-scale composting facility. Size-related abundance and communities of airborne bacteria as well as human pathogenic bacteria (HPB) were investigated using 16S rRNA gene sequencing coupled with droplet digital PCR. Our results indicate that the bacterial concentrations from the eight stages were approximately 104–105copies/m3. Although no statistical correlation was detected between the particle size and the Shannon index, the influence of size on bacterial lineages was observed in both composting and packaging areas. For airborne bacteria from different stages, the dominant phyla were Firmicutes, Proteobacteria, and Actinobacteria, and the dominant genera was Bacillus. Seven out of eight HPB with a small geometric mean aerodynamic diameter had a high concentration in composting areas. Based on diameters of 2.42 to 5.09 μm, most HPB in the composting areas were expected to be deposited on the bronchus and secondary bronchus. However, in the packaging areas, the deposition of HPB (diameters 3.70 to 8.96 μm) occurred in the upper part of the respiratory tract. Our results on the size distribution, abundance, and diversity of these bacteria offer important information for the systematic evaluation of bacterial pathogenicity and the potential health impacts on workers in composting plants and the surrounding residents. 相似文献