Chromosomal integration of bla CTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion

ABSTRACT The global CTX-M pandemic is considered a plasmid-driven phenomenon, yet chromosomal integration of bla CTX-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 bla CTX-M . Chromosomal integration was strongly structured by E. coli lineage and CTX-M variant, reaching 68.5% in ST38 and 43.9% in ST131. In the latter, integration rates varied between subclades with modelling, suggesting recent acceleration within the ST131-C2 subclade. Additional resistance genes were frequently co-integrated with bla CTX-M (33%), with architectures largely inherited from plasmid-borne structures. Integrations were mainly IS Ecp1 - or IS 26 -mediated (77.3% and 18.9%, respectively) and occurred across the entire E. coli chromosome without spared zones. bla CTX-M chromosomal integration is a widespread, lineage-structured component of the CTX-M pandemic, providing stable vertical inheritance that complements or may supplant plasmid-mediated dissemination in successful ESBL- E. coli clones.