Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli

International travel contributes significantly to the spread of extended-spectrum β-lactamase (ESBL) gene positive Escherichia coli (ESBL-Ec). We investigated bacterial determinants associated with persistence of ESBL-Ec after acquisition during international travel using short-and long read whole genome sequencing.

Our results show that sequence type 131 (ST131) and phylogroup D Escherichia coli are overrepresented in long-term carriers (≥12 months) compared to age, sex and travel destination matched short-term carriers (<1 month). ESBL-Ec clonal persistence is more prevalent than ESBL-plasmid persistence across multiple bacterial clones. Additionally, we describe two clonal lineages of ST38 which we detected using a novel open-source pipeline (https://github.com/boasvdp/SNP-distance-analysis) for the analysis of strain persistence in longitudinal bacterial sampling studies.

Further analyses show that ESBL-positive ST38 lineages have disseminated globally in recent years and are present in various recent public datasets from healthy and diseased humans indicating their rapid global emergence.