Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming

Peng, Zixin; Maciel-Guerra, Alexandre; Baker, Michelle; Zhang, Xibin; Hu, Yue; Wang, Wei; Rong, Jia; Zhang, Jing; Xue, Ning; Barrow, Paul; Renney, David; Stekel, Dov; Williams, Paul; Liu, Longhai; Chen, Junshi; Li, Fengqin; Dottorini, Tania

Abstract

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 bcombines 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 antimicrobial resistance (AMR) 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 ARGs 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 AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species.

Citation

Peng, Z., Maciel-Guerra, A., Baker, M., Zhang, X., Hu, Y., Wang, W., …Dottorini, T. (2022). Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Computational Biology, 18(3), Article e1010018. https://doi.org/10.1371/journal.pcbi.1010018

• Journal Article Type: Article
• Acceptance Date: Mar 14, 2022
• Online Publication Date: Mar 25, 2022
• Publication Date: Mar 1, 2022
• Deposit Date: Apr 7, 2022
• Publicly Available Date: Apr 7, 2022
• Journal: PLoS Computational Biology
• Print ISSN: 1553-734X
• Electronic ISSN: 1553-7358
• Publisher: Public Library of Science (PLoS)
• Peer Reviewed: Peer Reviewed
• Volume: 18
• Issue: 3
• Article Number: e1010018
• DOI: https://doi.org/10.1371/journal.pcbi.1010018
• Keywords: Computational Theory and Mathematics; Cellular and Molecular Neuroscience; Genetics; Molecular Biology; Ecology; Modeling and Simulation; Ecology, Evolution, Behavior and Systematics
• Public URL: https://nottingham-repository.worktribe.com/output/7651501
• Publisher URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010018