2. Academic Validation
  3. Fitness costs of mobilised colistin resistance gene 3 (mcr-3): systematic review, epidemiological study, and functional analysis

Fitness costs of mobilised colistin resistance gene 3 (mcr-3): systematic review, epidemiological study, and functional analysis

  • EBioMedicine. 2025 Oct:120:105923. doi: 10.1016/j.ebiom.2025.105923.
Lujie Liang 1,  Yaxin Li 1,  Lin Wang 2,  Wenli Wang 1,  Yihao Zhang 3,  Hui Zhao 4,  Yaxuan Wang 1,  Lingxuan Lyu 1,  Jiachen Li 1,  Dianrong Zhou 1,  Zhe Hu 5,  Lizhen Luo 5,  Guanxiu Wang 5,  Jia Wan 1,  Lin Xu 1,  Meisong Li 6,  Min Dai 7,  Meiting Yang 1,  Shun Xiong 1,  Lan-Lan Zhong 8,  Fang Bai 9,  Siyuan Feng 10,  Guo-Bao Tian 11
Affiliations

Affiliations

  • 1 Department of Immunology, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, Guangdong, China; Advanced Medical Technology Centre, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Programme in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China.
  • 2 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China.
  • 3 Division of Molecular Oncology, Graduate School of Medicine, Nagoya University, Aichi, Japan.
  • 4 Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China.
  • 5 College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
  • 6 Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
  • 7 School of Laboratory Medicine, Chengdu Medical College, Chengdu, China.
  • 8 Department of Immunology, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, Guangdong, China; Advanced Medical Technology Centre, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Programme in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China. Electronic address: lanlanzhong74@163.com.
  • 9 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China. Electronic address: baifang@shanghaitech.edu.cn.
  • 10 Advanced Medical Technology Centre, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Programme in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China. Electronic address: fsy0593@163.com.
  • 11 Department of Immunology, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, Guangdong, China; Advanced Medical Technology Centre, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Programme in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Guangzhou, 510060, China. Electronic address: tiangb@mail.sysu.edu.cn.
PMID: 40945051 DOI: 10.1016/j.ebiom.2025.105923
Abstract

Background: The rapid evolution and dissemination of mobilised colistin resistance gene (mcr) family has revealed as a severe threat to the global public health. Nevertheless, dramatic reduction in the prevalence of mcr-1, the major member of mcr family, was observed after the withdrawal of colistin in animal fodder in China since 2017, demonstrating that colistin acts as a selective stress to promote the dissemination of mcr-1. As the second largest lineage, mcr-3 was firstly discovered in 2017 and has been identified from numerous sources. However, whether the spreading of mcr-3 is driven by colistin remains unknown.

Methods: To this end, we investigated the global prevalence of mcr-3 from 2005 to 2022 by an up-to-date systematic review, along with a nation-wide epidemiological study to establish the change of mcr-3 prevalence in China before and after 2017. To investigate the fitness cost imposed by MCR-3 upon Bacterial host, in vitro and in vivo competitive assays were employed, along with morphological study and fluorescent observation. Moreover, by replacing non-optimal codons with optimal codons, synonymous mutations were introduced into the 5'-coding regions of mcr-3 to study mechanisms accounting for the distinct fitness cost conferred by MCR-1 and MCR-3. Furthermore, by combining AlphaFold and molecular dynamics (MD) simulation, we provided a complete characterisation on the putative lipid A binding pocket localised at the linker domain of MCR-3. Crucially, inhibitors targeting at the putative binding pocket of MCR-1 or MCR-3 were identified from small molecules library using the pipeline of virtual screening.

Findings: The global prevalence of mcr-3 increased continuously from 2005 to 2022. The average prevalence was 0.18% during 2005-2014 and rapidly increased to 3.41% during 2020-2022. The prevalence of mcr-3 in China increased from 0.79% in 2016 to 5.87% in 2019. We found that the fitness of mcr-3-bearing Escherichia coli and empty plasmid control was comparable but higher than that of mcr-1-positive strain. Although the putative lipid A binding pocket of MCR-3 was similar to that of in MCR-1, mcr-3 occupies remarkable codon bias at the 5'-end of coding region that disrupted the stability of mRNA, further reduced its protein expression in E. coli, resulting in the low fitness burden of Bacterial host. Moreover, the 5'-end codon usage frequency appeared as a critical factor related with the evolution of mcr family. Furthermore, based on the similar lipid A binding pocket among MCR family protein, we identified three MCR inhibitors targeting at such pocket by screening from small-molecule library, which effectively restored the colistin susceptibility of mcr-bearing E. coli.

Interpretation: We found that the prevalence of mcr-3 increased continuously during 2016-2019 in China, demonstrating that the withdrawal of colistin in husbandry failed to prevent the dissemination of mcr-3. Our study evidenced that the 5'-end codon bias appeared as a crucial regulator upon the fitness cost conferred by horizontally transferred genes. Most importantly, the putative lipid A binding pocket verified from current study was a promising target site for designing inhibitors against mcr-positive strains.

Funding: Natural Science Foundation of China, National Key Research and Development Programme of China.

Keywords

Colistin; Fitness; MCR inhibitors; Prevalence; mcr-1; mcr-3.

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