Putative mobilized colistin resistance genes in the human gut microbiome

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.

Keywords: Antibiotic resistance genes; Colistin; Human microbiome; MCR; Metagenomics.

Fig. 1

Relative prevalence of mcr-like genes in countries with at least 50 genomes in the study. Bubble area shows the number of genes divided by the number of genomes from each country

Fig. 2

Prevalence of mcr-like genes in different species (with 10 or more mcr-like genes) in MAGs and isolates

Fig. 3

PAP2-domain in mcr-like gene from Sutterella wadsworthensis. Comparison with E. coli mcr-1 gene including the PAP2-like phosphatase gene downstream. PAP2-domains are colored turquoise, mcr-like gene/regions red. Predicted transmembrane helices (TMHMM 2.0 server) are indicated as black bars

Fig. 4

Number of ARGs per class co-occurring in the same genome with Mcr-like genes

Fig. 5

Phylogenetic tree of MCR-like sequences. We used only sequences present in contigs classified as plasmids and we clusterized similar sequences with CD-HIT on 97% similarity. The phylogenetic informative regions were selected by BMGE and the Maximum likelihood (ML) phylogenetic tree was calculated by PhyML 3.0 with the model selection performed by SMS (AIC method) and 100 bootstrap replicates to infer significance. We added clinical MCR sequences from NCBI to the analysis (preceded by an accession number starting with WP). UHGG sequences predicted to be located on a plasmid by PlasFlow contain the “plasmid” note