<i>mcr-9</i> , an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin

Abstract

The plasmid-located <i>mcr-9</i> gene, encoding a putative phosphoethanolamine transferase, was identified in a colistin-resistant human fecal <i>Escherichia coli</i> strain belonging to a very rare phylogroup, the D-ST69-O15:H6 clone. This MCR-9 protein shares 33% to 65% identity with the other plasmid-encoded MCR-type enzymes identified (MCR-1 to -8) that have been found as sources of acquired resistance to polymyxins in <i>Enterobacteriaceae</i> Analysis of the lipopolysaccharide of the MCR-9-producing isolate revealed a function similar to that of MCR-1 by adding a phosphoethanolamine group to lipid A and subsequently modifying the structure of the lipopolysaccharide. However, a minor impact on susceptibility to polymyxins was noticed once the <i>mcr-9</i> gene was cloned and produced in an <i>E. coli</i> K-12-derived strain. Nevertheless, we showed here that subinhibitory concentrations of colistin induced the expression of the <i>mcr-9</i> gene, leading to increased MIC levels. This inducible expression was mediated by a two-component regulatory system encoded by the <i>qseC</i> and <i>qseB</i> genes located downstream of <i>mcr-9</i> Genetic analysis showed that the <i>mcr-9</i> gene was carried by an IncHI2 plasmid. <i>In silico</i> analysis revealed that the plasmid-encoded MCR-9 shared significant amino acid identity (ca. 80%) with the chromosomally encoded MCR-like proteins from <i>Buttiauxella</i> spp. In particular, <i>Buttiauxella gaviniae</i> was found to harbor a gene encoding MCR-BG, sharing 84% identity with MCR-9. That gene was neither expressed nor inducible in its original host, which was fully susceptible to polymyxins. This work showed that <i>mcr</i> genes may circulate silently and remain undetected unless induced by colistin.