Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127

Paarthiphan Elankumaran; Glenn F Browning; Marc S Marenda; Cameron J Reid; Steven P Djordjevic

doi:10.1016/j.crmicr.2022.100106

Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127

Curr Res Microb Sci. 2022 Jan 23:3:100106. doi: 10.1016/j.crmicr.2022.100106. eCollection 2022.

Authors

Paarthiphan Elankumaran¹, Glenn F Browning², Marc S Marenda², Cameron J Reid¹, Steven P Djordjevic¹

Affiliations

¹ iThree Institute, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia.
² Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville and Werribee, Victoria, Australia.

Abstract

Escherichia coli ST127, a recently emerged global pathogen noted for high virulence gene carriage, is a leading cause of urinary tract and blood stream infections. ST127 is frequently isolated from humans and companion animals; however, it is unclear if they are distinct or related populations of ST127. We performed a phylogenomic analysis of 299 E. coli ST127 of diverse epidemiological origin to characterize their population structure, genetic determinants of virulence, antimicrobial resistance, and repertoire of mobile genetic elements with a focus on plasmids. The core gene phylogeny was divided into 13 clusters, the largest of which (BAP4) contained the majority of human and companion animal origin isolates. This dominant cluster displayed genetic differences to the remainder of the phylogeny, most notably alternative gene alleles encoding important virulence factors including lipid A, flagella, and K capsule. Furthermore, numerous close genetic linkages (<30 SNPs) between human and companion animal isolates were observed within the cluster. Carriage of antimicrobial resistance genes in the collection was limited, but virulence gene carriage was extensive. We found evidence of pUTI89-like virulence plasmid carriage in over a third of isolates, localised to four of the major phylogenetic clusters. Our study supports global scale repetitive transfer of E. coli ST127 lineages between humans and companion animals, particularly within the dominant BAP4 cluster.

Keywords: Antibiotic resistance; Companion animals; E. coli; E. coli virulence; ExPEC; Extraintestinal pathogenic E. coli; Genomic epidemiology; Interspecies E. coli transfer; One Health; Phylogenomics; ST127.