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Genomic epidemiology of major extra-intestinal pathogenic Escherichia coli lineages causing urinary tract infections in young women across Canada Fibke, Chad

Abstract

Urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Extra-intestinal pathogenic Escherichia coli (ExPEC) are responsible for more than 80% of UTIs. ExPEC have been isolated from the environment, food sources and companion animals. Once acquired from an external source, ExPEC asymptomatically colonize the intestinal tract, and act as an immediate reservoir for subsequent extra-intestinal infection. Despite considerable ExPEC diversity, only a few multi-locus sequence types (STs) cause the majority of infections. Our study examines the population structure and exposures associated with UTI caused by major ExPEC lineages. A total of 385 women with community-acquired UTI caused by E. coli across Canada were questioned about their diet, travel and other exposure history. Genome sequencing was used to determine both ST and genomic similarity. ST69, ST73, ST95, ST127 and ST131 were responsible for 54% of all UTIs. Seven UTI clusters were identified, but genomes from the ST95 and ST420 clusters exhibited fewer than 4 single nucleotide variations, suggesting recent transmission from a common source. The predominant STs were all associated with consumption of high-risk foods such as seafood and raw meat, and all STs, except for ST73, were associated with travel. These results suggest specific exposures exist for pandemic ExPEC lineages. Identifying the reservoirs of common, community-acquired ExPEC lineages will aid our understanding of the evolution, emergence, and dissemination of high-risk clones within the community setting.

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