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A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coliwere found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coliisolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

Bioretention facilities are common source reduction facilities, but traditional fillers are not effective in reducing emerging contaminants such as antibiotics. Although Fe-Mn oxides have been extensively explored, their removal of emerging contaminants and application in the sponge city have not yet been addressed. Therefore, this study aims to address this limitation by developing Fe-Mn oxide fillers. In this research, the optimal preparation conditions (Fe/Mn mole ratio, polyvinyl alcohol (PVA) concentration, and filler particle size) and influencing factors (filler dosage, initial pollutant concentration, pH, temperature, and co-existing ions) were investigated using a typical antibiotic, norfloxacin (NOR), as the target contaminant. The removal mechanism of NOR was investigated by SEM, FTIR, and XPS characterizations. Subsequently, the fillers were applied to bioretention facilities with different filling modes (layered and mixed) to evaluate their effectiveness in removing NOR and conventional pollutants at different recurrence periods, drought periods, and pollutant influent concentrations. The study indicated that Fe-Mn oxide filler (Fe/Mn mole ratio of 4:1, PVA concentration of 7 %, particle size of 4 mm) could remove more than 70 % of NOR (1–20 mg/L). The NOR removal by Fe-Mn oxide filler involved adsorption and redox reactions. Notably, bioretention facilities using Fe-Mn oxide fillers have shown varying degrees of improvement in the removal of NOR and conventional pollutants compared to conventional ones. This study contributes to the application of Fe-Mn oxide filler in bioretention facilities, thus playing a crucial role in mitigating antibiotic pollution in stormwater runoff.

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coliwere found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coliisolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

This study investigated the microbial contamination of ice cream in China. A total of 2887 ice cream samples were collected from different regions of China. Contamination by the aerobic plate count (APC), coliforms, and three foodborne pathogens, Listeria monocytogenes(L. monocytogenes), Staphylococcus aureus(S. aureus), and Salmonellaspp., was detected in the samples. L. monocytogenesisolates were further analyzed for antibiotic susceptibility and multi-locus sequence typing (MLST). The results showed that APC was more than 105colony forming units (CFU)/g in 6.10% (176/2887) and coliform was more than 102CFU/g in 15.69% (453/2887) of all samples. The positive rates of S. aureus, L. monocytogenes, and Salmonellaspp. were 0.66%, 0.62%, and 0.10%, respectively. Among these, S. aureuscontamination was more than 102CFU/g in two samples, and L. monocytogenesin the positive sample was in the range of 0.3–240 most probable number (MPN)/g, with a median of 4.3 MPN/g. The hygienic status of the packaged samples was much better than that of the bulk samples (P<0.05). Catering samples were more frequently and heavily contaminated than samples from retail and wholesale outlets (P<0.05). No significant differences were observed in samples bought from urban and rural areas (P>0.05). For 18 L. monocytogenesstrains isolated from ice cream, the resistance rate of nine antibiotics was 5.56% (1/18). By MLST, the L. monocytogenesstrains were classified into nine sequence types (STs), of which ST8 was the most common (six isolates). These results indicate that a potential health risk to the public may be caused by ice cream, particularly in susceptible populations.