Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion
The global CTX-M pandemic is considered a plasmid-driven phenomenon, yet chromosomal integration of blaCTX-M has been reported in various settings. Screening 451,174 publicly available E. coli genomes and retaining 2,269 CTX-M-E. coli long-read or hybrid assemblies, we found that 33.5% carried at least one chromosomally integrated blaCTX-M. Chromosomal integration was strongly structured by E.…
A global CTX-M pandemic, driven by plasmids, has recently shown evidence of chromosomal integration of blaCTX-M in E. coli, according to a study analyzing 451,174 publicly available E. coli genomes. Of the 2,269 CTX-M-E. coli long-read or hybrid assemblies, 33.5% contained at least one chromosomally integrated blaCTX-M gene. This chromosomal integration was strongly correlated with the E. coli lineage and the specific CTX-M variant, reaching 68.5% in the ST38 lineage and 43.9% in the ST131 lineage.
The integration rates varied between subclades of ST131, indicating a recent acceleration in the ST131-C2 subclade. In addition to the blaCTX-M gene, these chromosomal integrations frequently included other resistance genes, with architectures largely inherited from plasmid-borne structures. The ISEcp1- and IS26-mediated integrations occurred throughout the entire E. coli chromosome without any spared zones.
The chromosomal integration of blaCTX-M is a widespread and lineage-structured component of the CTX-M pandemic, providing stable vertical inheritance that complements or may even replace plasmid-mediated dissemination in successful ESBL-E. coli clones.
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