Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada

Chad D Fibke; Matthew A Croxen; Hyun Min Geum; Magdalena Glass; Eugenia Wong; Brent P Avery; Danielle Daignault; Michael R Mulvey; Richard J Reid-Smith; E Jane Parmley; Andrea Portt; Patrick Boerlin; Amee R Manges

doi:10.1093/ofid/ofz431

Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada

Open Forum Infect Dis. 2019 Oct 9;6(11):ofz431. doi: 10.1093/ofid/ofz431. eCollection 2019 Nov.

Authors

Chad D Fibke¹, Matthew A Croxen^{2

3}, Hyun Min Geum¹, Magdalena Glass¹, Eugenia Wong⁴, Brent P Avery⁵, Danielle Daignault⁶, Michael R Mulvey^{7

8}, Richard J Reid-Smith^{5

9}, E Jane Parmley^{5

9}, Andrea Portt¹⁰, Patrick Boerlin¹¹, Amee R Manges^{1

12}

Affiliations

¹ School of Population and Public Health, The University of British Columbia, Vancouver, BC, Canada.
² Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada.
³ Public Health Laboratory (ProvLab), Edmonton, AB, Canada.
⁴ Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada.
⁵ Center for Food-borne, Environmental and Zoonotic Infectious Disease, Public Health Agency of Canada, Guelph, ON, Canada.
⁶ National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, QC, Canada.
⁷ Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada.
⁸ National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
⁹ Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
¹⁰ Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
¹¹ Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.
¹² British Columbia Centre for Disease Control, Vancouver, BC, Canada.

Abstract

Background: A few extraintestinal pathogenic Escherichia coli (ExPEC) multilocus sequence types (STs) cause the majority of community-acquired urinary tract infections (UTIs). We examine the genomic epidemiology of major ExPEC lineages, specifically factors associated with intestinal acquisition.

Methods: A total of 385 women with UTI caused by E. coli across Canada were asked about their diet, travel, and other exposures. Genome sequencing was used to determine both ST and genomic similarity. Logistic regression was used to identify factors associated with the acquisition of and infection with major ExPEC STs relative to minor ExPEC STs.

Results: ST131, ST69, ST73, ST127, and ST95 were responsible for 54% of all UTIs. Seven UTI clusters were identified, but genomes from the ST95, ST127, and ST420 clusters exhibited as few as 3 single nucleotide variations across the entire genome, suggesting recent acquisition. Furthermore, we identified a cluster of UTIs caused by 6 genetically-related ST1193 isolates carrying mutations in gyrA and parC. The acquisition of and infection with ST69, ST95, ST127, and ST131 were all associated with increased travel. The consumption of high-risk foods such as raw meat or vegetables, undercooked eggs, and seafood was associated with acquisition of and infection with ST69, ST127, and ST131, respectively.

Conclusions: Reservoirs may aid in the dissemination of pandemic ExPEC lineages in the community. Identifying ExPEC reservoirs may help prevent future emergence and dissemination of high-risk lineages within the community setting.

Keywords: antimicrobial resistance; extraintestinal pathogenic Escherichia coli; food safety; molecular epidemiology; urinary tract infections.