Extraintestinal pathogenic lineages of extended-spectrum β-lactamase (ESBL)-producing E. coli are associated with prolonged ESBL gene carriage

Objectives: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) are frequently acquired during international travel, contributing to the global spread of antimicrobial resistance. Human-adapted ESBL-Ec are predicted to exhibit increased intestinal carriage duration, resulting in a higher likelihood of onward human-to-human transmission. Yet, bacterial determinants of increased carriage duration are unknown. Previous studies analysed small traveler cohorts, with short follow-up times, or did not employ high-resolution molecular typing, and were thus unable to identify bacterial traits associated with long-term carriage after recent acquisition. We aimed to identify which ESBL-Ec lineages are associated with increased carriage duration after return from international travel. Methods In a prospective cohort study of 2001 international travelers, we analysed 160 faecal ESBL-Ec isolates from all 38 travelers who acquired ESBL-Ec during travel and subsequently carried ESBL-Ec for at least 12 months after return, by whole-genome sequencing. For 17 travelers, we confirmed the long-term carriage of ESBL-Ec strains through single nucleotide variant typing. To identify determinants of increased carriage duration, we compared the 17 long-term carriers (≥12 months carriage) with 33 age-, sex- and destination-matched short-term carriers (<1 month carriage). Long read sequencing was employed to investigate long-term ESBL plasmid carriage. Results We show that in healthy travelers with very low antibiotic usage, extraintestinal pathogenic lineages of E. coli (ExPEC) are significantly more likely to persist than other E. coli lineages. The long-term carriage of E. coli from ExPEC lineages is mainly driven by sequence type 131 and phylogroup D E. coli. Conclusions Although ExPEC lineages frequently cause extra-intestinal infections such as bloodstream infections, our results indicate that ExPEC lineages are also efficient intestinal colonisers, which potentially contributes to their onward transmission.