Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Baker, Michelle; Zhang, Xibin; Maciel-Guerra, Alexandre; Babaarslan, Kubra; Dong, Yinping; Wang, Wei; Hu, Yujie; Renney, David; Liu, Longhai; Li, Hui; Hossain, Muhammad; Heeb, Stephan; Tong, Zhiqin; Pearcy, Nicole; Zhang, Meimei; Geng, Yingzhi; Zhao, Li; Hao, Zhihui; Senin, Nicola; Chen, Junshi; Peng, Zixin; Li, Fengqin; Dottorini, Tania

Abstract

Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using novel data-mining methods. Most isolates within same hosts possessed same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Machine learning revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials and primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

Citation

Baker, M., Zhang, X., Maciel-Guerra, A., Babaarslan, K., Dong, Y., Wang, W., Hu, Y., Renney, D., Liu, L., Li, H., Hossain, M., Heeb, S., Tong, Z., Pearcy, N., Zhang, M., Geng, Y., Zhao, L., Hao, Z., Senin, N., Chen, J., …Dottorini, T. (2024). Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nature Communications, 15, Article 206. https://doi.org/10.1038/s41467-023-44272-1

• Journal Article Type: Article
• Acceptance Date: Dec 6, 2023
• Online Publication Date: Jan 5, 2024
• Publication Date: Jan 5, 2024
• Deposit Date: Nov 27, 2023
• Publicly Available Date: Jan 9, 2024
• Journal: Nature Communications
• Electronic ISSN: 2041-1723
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Article Number: 206
• DOI: https://doi.org/10.1038/s41467-023-44272-1
• Public URL: https://nottingham-repository.worktribe.com/output/27858919
• Publisher URL: https://www.nature.com/articles/s41467-023-44272-1
• Additional Information: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.