Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
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Published:2024-01-05
Issue:1
Volume:15
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Baker Michelle, Zhang Xibin, Maciel-Guerra Alexandre, Babaarslan Kubra, Dong Yinping, Wang Wei, Hu YujieORCID, Renney David, Liu Longhai, Li Hui, Hossain Maqsud, Heeb StephanORCID, Tong Zhiqin, Pearcy Nicole, Zhang Meimei, Geng Yingzhi, Zhao Li, Hao Zhihui, Senin NicolaORCID, Chen Junshi, Peng ZixinORCID, Li Fengqin, Dottorini TaniaORCID
Abstract
AbstractSharing 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.
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
Reference120 articles.
1. O’Neill, J. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations (The Review on Microbial Resistance, 2016) 2. Bottery, M. J., Pitchford, J. W. & Friman, V. P. Ecology and evolution of antimicrobial resistance in bacterial communities. ISME J. 15, 939–948 (2021). 3. Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088–00017 (2018). 4. Davies, N. G., Flasche, S., Jit, M. & Atkins, K. E. Within-host dynamics shape antibiotic resistance in commensal bacteria. Nat. Ecol. Evol. 3, 440–449 (2019). 5. Ewers, C., Antão, E.-M., Diehl, I., Philipp, H.-C. & Wieler, L. H. Intestine and environment of the chicken as reservoirs for extraintestinal pathogenic Escherichia coli strains with zoonotic potential. Appl. Environ. Microbiol. 75, 184–192 (2009).
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