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.

Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 ‘superplasmids’ in clinical carbapenem-resistant Enterobacterales

“…For E. hormaechei ST93 and ST190 median pairwise single nucleotide variant (SNV) distance was 8 SNVs (IQR 2-16) and 2 SNVs (IQR 1-2), respectively (Figure S1). In contrast, E. hormaechei ST114 had a median pairwise SNV distance of 28 SNVs (IQR [23][24][25][26][27][28][29][30][31][32][33][34][35][36]. For all clones, the low SNV distances are suggestive of intra-institutional spread.…”

Involvement of hpap2 and dgkA Genes in Colistin Resistance Mediated by mcr Determinants

“…Interestingly, a recent study evidenced that, among 64628 genomes deposited in NCBI databases and screened for mcr sequences, three of the less commonly found genes lack hpap2- or dgkA -linked sequences, like mcr-4 and mcr-5 , or are clustered to a truncated hpap2 coding sequence in the even more rarely found mcr-2 gene [ 13 ]. Furthermore, mcr-9 and mcr-10 , the two last and most closely related mcr genes identified so far, lacked both hpap2 or dgkA linked sequences and, although globally spread, had a weak role in colistin resistance [ 11 , 13 , 14 ]. Thus, mcr-1 and mcr-3 are the colistin resistance determinants more frequently mobilized, with plasmids carrying mcr-1–hpap2 or mcr-3–dgkA widely distributed among different species.…”

Complementarity of Selective Culture and qPCR for Colistin Resistance Screening in Fresh and Frozen Pig Cecum Samples

“…After identification, molecular characterization of the isolates was carried out by a conventional PCR to analyze the presence of colistin resistance mcr genes ( mcr-1 to 5) ( Rebelo et al, 2018 ). As described in literature, mcr-6 seems to be an endogenous gene from Moraxella spp., mcr-7 was only described in Klebsiella spp., mcr-8 was identified in Klebsiella pneumoniae and Raoutella ornithinolitica and mcr-9 and mcr-10 do not seem to confer resistance to colistin ( Khedher et al, 2020 ; Wang et al, 2020 ). Therefore, we focused on genes mcr-1 to 5 since they have been described in different bacterial genera and have not been linked to a particular bacterial group.…”

“…Since the first description of a plasmid-mediated colistin resistance determinant in 2015 (mcr-1), up to ten mcr-related genes have been described. However, mcr-1 still remains as the most common colistin resistance determinant carried by plasmids since it is present worldwide, especially in Escherichia coli of human and animal origin (Khedher et al, 2020;Wang et al, 2020); therefore, in this study we took mcr-1 as an indicator of acquired colistin resistance. Many retrospective studies screened colistin resistance (both bacteria and genes) over bacterial strain collections (Carattoli et al, 2017;Garcia et al, 2018;Migura-Garcia et al, 2019), but they were rarely performed on biological samples (Miguela-Villoldo et al, 2019).…”