Whole genome sequencing and phylogenetic analysis to examine acquisition of Escherichia coli clones during international travel

Abstract

International travel facilitates the acquisition and carriage of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E). We describe genomes of predominant ESBL-E clones detected before and after travel among subjects departing from Rio de Janeiro, Brazil, during 2015-2021, and genomes publicly available from countries visited by travelers. WGS (Illumina NovaSeq) was performed on 70 ESBL-E isolates from 66 travelers (18 pre- and 52 post-travel). Sequence type (ST), antimicrobial resistance (AMR), virulence genes, and plasmids were determined by Center for Genomic Epidemiology tools. Phylogenetic trees were constructed with each of the most frequent ST of travelers’ genomes (TG) and genomes with the same ST from Enterobase (EG). Other analyses were performed with Prokka, Roary, SNP-sites, and FastTree. Trees were visualized with iTOL. Among 70 ESBL-E, the clonal composition was quite diverse, with 41 different ST, with predominance before of CC10 and CC131, and after travel, CC10, CC131, CC69, and CC38, and three ST described for the first time: ST14408 and ST14412 (CC10), and ST4411 (CC20). Core genome phylogenetic analysis revealed 17 clusters, eight of which formed by post-travel TG and EG detected in the same country visited by traveler. We observed an increased number and diversity of AMR genes, plasmids, and virulence genes in post-travel isolates, although we only found statistical significance for IncFIB plasmid. Genome clustering supported the high-risk clone acquisition and AMR during international trips. More than half of detected clones were related to ExPEC and showed an increased number and diversity of AMR and virulence-related genes, as well as plasmids in post-travel isolates.