Analysis of Serial Isolates of <i>mcr-1</i> -Positive Escherichia coli Reveals a Highly Active IS <i>Apl1</i> Transposon

Abstract

The emergence of a transferable colistin resistance gene (<i>mcr-1</i>) is of global concern. The insertion sequence IS<i>Apl1</i> is a key component in the mobilization of this gene, but its role remains poorly understood. Six <i>Escherichia coli</i> isolates were cultured from the same patient over the course of 1 month in Germany and the United States after a brief hospitalization in Bahrain for an unconnected illness. Four carried <i>mcr-1</i> as determined by real-time PCR, but two were negative. Two additional <i>mcr-1</i>-negative <i>E. coli</i> isolates were collected during follow-up surveillance 9 months later. All isolates were analyzed by whole-genome sequencing (WGS). WGS revealed that the six initial isolates were composed of two distinct strains: an initial ST-617 <i>E. coli</i> strain harboring <i>mcr-1</i> and a second, unrelated, <i>mcr-1</i>-negative ST-32 <i>E. coli</i> strain that emerged 2 weeks after hospitalization. Follow-up swabs taken 9 months later were negative for the ST-617 strain, but the <i>mcr-1</i>-negative ST-32 strain was still present. <i>mcr-1</i> was associated with a single copy of IS<i>Apl1</i>, located on a 64.5-kb IncI2 plasmid that shared >95% homology with other <i>mcr-1</i> IncI2 plasmids. IS<i>Apl1</i> copy numbers ranged from 2 for the first isolate to 6 for the final isolate, but IS<i>Apl1</i> movement was independent of <i>mcr-1</i> Some movement was accompanied by gene disruption, including the loss of genes encoding proteins involved in stress responses, arginine catabolism, and l-arabinose utilization. These data represent the first comprehensive analysis of IS<i>Apl1</i> movement in serial clinical isolates and reveal that, under certain conditions, IS<i>Apl1</i> is a highly active IS element whose movement may be detrimental to the host cell.