Horizontal gene transfer facilitates the spread of antibiotic resistance genes, which constitutes a global challenge. However, the evolutionary trajectory of the mobile colistin resistome in bacteria is largely unknown. To investigate the coevolution and fitness cost of the colistin resistance genes in wild strains, different assays to uncover the genomic dynamics ofmcr‐1 andmcr‐3 in bacterial populations are utilized.Escherichia coli strains harboring bothmcr‐1 andmcr‐3.1/3.5 are isolated andmcr genes are associated with diverse mobile elements. Under exposure to colistin, themcr‐1 ‐bearing resistome is stably inherited during bacterial replication, butmcr‐3 is prone to be eliminated in populations of certain strains. In the absence of colistin, the persistence rates of themcr‐1 andmcr‐3 ‐bearing subclones varies depending on the genomic background. The decay of themcr ‐bearing bacterial populations can be mediated by the elimination ofmcr ‐containing segments, large genomic deletions, and plasmid loss. Mobile elements, including plasmids and transposons, are double‐edged swords in the evolution of the resistome. The findings support the idea that antibiotic overuse accounts for global spread of multidrug‐resistant (MDR) bacteria. Therefore, stringent regulation of antibiotic prescription for humans and animals should be performed systematically to alleviate the threat of MDR bacteria. The evolutionary trajectory of mobile colistin resistance genes and the underlying genomic basis in bacteria are largely unknown after withdrawal of colistin from animal feed additives. This study comprehensively deciphers the genomic landscape after the elimination ofmcr genes during bacterial growth under different conditions, highlighting the pivotal role of mobile elements in mediating resistance gene transmission.
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