Massive analysis of 64,628 bacterial genomes to decipher water reservoir and origin of mobile colistin resistance genes: is there another role for these enzymes?

Abstract

Since 2015, new worrying colistin resistance mechanism, mediated by mcr-1 gene has been reported worldwide along with eight newly described variants but their source(s) and reservoir(s) remain largely unexplored. Here, we conducted a massive bioinformatic analysis of bacterial genomes to investigate the reservoir and origin of mcr variants. We identified 13'658 MCR-1 homologous sequences in 494 bacterial genera. Moreover, analysis of 64'628 bacterial genomes (60 bacterial genera and 1'047 species) allows identifying a total of 6'651 significant positive hits (coverage >90% and similarity >50%) with the nine MCR variants from 39 bacterial genera and more than 1'050 species. A high number of MCR-1 was identified in Escherichia coli (n = 862). Interestingly, while almost all variants were identified in bacteria from different sources (i.e. human, animal, and environment), the last variant, MCR-9, was exclusively detected in bacteria from human. Although these variants could be identified in bacteria from human and animal sources, we found plenty MCR variants in unsuspected bacteria from environmental origin, especially from water sources. The ubiquitous presence of mcr variants in bacteria from water likely suggests another role in the biosphere of these enzymes as an unknown defense system against natural antimicrobial peptides and/or bacteriophage predation.

Figure 1

General representation of the distinctive homologous MCR sequences. (A) Phylogenetic tree inferred from PETs sequences from different bacterial species and highlighting MCR-1 to MCR-9 group using Archaeopteryx software. Protein identity of MCR-1 with all homologous sequence is indicated, lowest and highest % identity are indicated for each genus. Only representative bacterial genera are shown on this figure. (B) General features of known MCR variants including their phylogenetic relationship, nucleotide size and %CG content. Pairwise comparison of amino acid identity of MCR variants is also presented. (C) Rhizome analysis of MCR-1. This latter is here split into fragment of 50 aa and phylogenetic tree inferred for each fragment. Each presented line (blue and red) refer to the putative closest ancestor of each corresponding fragment. 8 out of the 11 fragments appeared from M. pluranimalium species.

Figure 2

Phylogenetic subtrees highlighting the position of known MCR variants relative to the other species. (A) Phylogenetic subtree of MCR-1; MCR-2 and MCR-6; (B) Subtree of MCR-3, MCR-7, and MCR-9; (C) subtree of MCR-4; (D) subtree of MCR-5; and (E) subtree of MCR-8. The average percentage of aa identity with MCR variants are indicated.

Figure 3

All bacterial genomes analysed here and the RpoB-based phylogenetic tree of all investigated bacterial species. Bacterial species identified as MCR-producers and the number of significant MCR hits are highlighted in red. The number of species and genomes analyzed (complete and Whole genome sequences) are also indicated. *, refers to rare bacterial species from the environment (list of the 27 genomes are given in Supplementary Table 1).

Figure 4

Network analysis of metadata of MCR variant producer isolates (excluding E. coli mcr-1) highlighting the link between each MCR variant and the different bacterial species and their isolation sources such as Human, Animal, and the Environment.