Putative mobilized colistin resistance genes in the human gut microbiome

BMC Microbiology

Rafael R. C. Cuadrat¹  Alberto M. R. Dávila²  Felipe H. Coutinho³  Haithem Afli⁴  Bruno G. N. Andrade⁴  Tobias Goris⁵ 

[1] Bioinformatics and Omics Data Science, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC);Computational and Systems Biology Laboratory and Graduate Program on Biodiversity and Health, Oswaldo Cruz Institute, FIOCRUZ;Departamento de producción vegetal y microbiología, Universidad Miguel Hernández;Department of Computer Science, Munster Technological University, MTU/ADAPT;Department of Molecular Toxicology, Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke – DIfE;

关键词: Colistin;    Human microbiome;    MCR;    Metagenomics;    Antibiotic resistance genes;   

DOI  :  10.1186/s12866-021-02281-4

来源: DOAJ

【 摘 要 】

Abstract Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

【 授权许可】

Unknown