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

Michelle Baker, Xibin Zhang, Alexandre Maciel-Guerra, Kubra Babaarslan, Yinping Dong, Wei Wang, Yujie Hu, David Renney, Longhai Liu, Hui Li, Maqsud Hossain, Stephan Heeb, Zhiqin Tong, Nicole Pearcy, Meimei Zhang, Yingzhi Geng, Li Zhao, Zhihui Hao, Nicola Senin, Junshi Chen, Zixin Peng (), Fengqin Li () and Tania Dottorini ()
Additional contact information
Michelle Baker: University of Nottingham, College Road, Sutton Bonington
Xibin Zhang: Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety
Alexandre Maciel-Guerra: University of Nottingham, College Road, Sutton Bonington
Kubra Babaarslan: University of Nottingham, College Road, Sutton Bonington
Yinping Dong: China National Center for Food Safety Risk Assessment
Wei Wang: China National Center for Food Safety Risk Assessment
Yujie Hu: China National Center for Food Safety Risk Assessment
David Renney: 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh
Longhai Liu: Shandong Kaijia Food Co. Ltd
Hui Li: No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province
Maqsud Hossain: University of Nottingham, College Road, Sutton Bonington
Stephan Heeb: University of Nottingham, East Drive
Zhiqin Tong: No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province
Nicole Pearcy: University of Nottingham, College Road, Sutton Bonington
Meimei Zhang: Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District
Yingzhi Geng: Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District
Li Zhao: College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District
Zhihui Hao: College of Veterinary Medicine, China Agricultural University, Haidian District
Nicola Senin: University of Perugia
Junshi Chen: China National Center for Food Safety Risk Assessment
Zixin Peng: China National Center for Food Safety Risk Assessment
Fengqin Li: China National Center for Food Safety Risk Assessment
Tania Dottorini: University of Nottingham, College Road, Sutton Bonington

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: 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 data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, 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.

Date: 2024
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DOI: 10.1038/s41467-023-44272-1

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