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Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to AR phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying AR genes across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species.

Lung cancer is the most frequently life-threatening disease and the prominent cause of cancer-related mortality among human beings worldwide, where poor early diagnosis and expensive detection costs are considered as significant reasons. Here, we try to tackle this issue by proposing a novel label-free and low-cost strategy for rapid detection and distinction of lung cancer cells relying on plasmonic toroidal metasurfaces at terahertz frequencies. Three disjoint regions are displayed in identifiable intensity-frequency diagram, which could directly help doctors determine the type of lung cancer cells for clinical treatment. The metasurface is generated by two mirrored gold split ring resonators with subwavelength sizes. When placing analytes on the metasurface, apparent shifts of both the resonance frequency and the resonance depth can be observed in the terahertz transmission spectra. The theoretical sensitivity of the biosensor over the reflective index reaches as high as 485.3 GHz/RIU. Moreover, the proposed metasurface shows high angular stability for oblique incident angle from 0 to 30°, where the maximum resonance frequency shift is less than 0.66% and the maximum transmittance variation keeps below 1.33%. To experimentally verify the sensing strategy, three types of non-small cell lung cancer cells (Calu-1, A427, and 95D) are cultured with different concentrations and their terahertz transmission spectra are measured with the proposed metasurface biosensor. The two-dimensional fingerprint diagram considering both the frequency and transmittance variations of the toroidal resonance dip is obtained, where the curves for different cells are completely separated with each other. This implies that we can directly distinguish the type of the analyte cells and its concentration by only single spectral measurement. We envisage that the proposed strategy has potential for clinical diagnosis and significantly expands the capabilities of plasmonic metamaterials in biological detection.