title: Household Clustering ofEscherichia coliSequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.
abstract: Background.Within-household sharing of strains from the resistance-associatedH30R1 andH30Rx subclones ofEscherichia colisequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis.Methods.Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates.Results.In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed betweenH30R1 andH30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member.Conclusions.Within-household sharing ofE coliST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.
authors.affiliation: Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis.
authors.forename: James R
authors.initials: JR
authors.lastname: Johnson
authors.affiliation: George Washington University , Washington, District of Columbia.
authors.forename: Gregg
authors.initials: G
authors.lastname: Davis
authors.affiliation: Minneapolis Veterans Affairs Health Care System , Minnesota.
authors.forename: Connie
authors.initials: C
authors.lastname: Clabots
authors.affiliation: Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Johnston
authors.affiliation: Minneapolis Veterans Affairs Health Care System , Minnesota.
authors.forename: Stephen
authors.initials: S
authors.lastname: Porter
authors.affiliation: The Pennsylvania State University , University Park.
authors.forename: Chitrita
authors.initials: C
authors.lastname: DebRoy
authors.affiliation: Children's Hospitals and Clinics of Minnesota , St. Paul.
authors.forename: William
authors.initials: W
authors.lastname: Pomputius
authors.affiliation: St. Luke's University Hospital and Health Network , Bethlehem, Pennsylvania.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Ender
authors.affiliation: University of Missouri , Columbia.
authors.forename: Michael
authors.initials: M
authors.lastname: Cooperstock
authors.affiliation: Minneapolis Veterans Affairs Health Care System , Minnesota.
authors.forename: Billie Savvas
authors.initials: BS
authors.lastname: Slater
authors.affiliation: Mayo Clinic , Rochester, Minnesota.
authors.forename: Ritu
authors.initials: R
authors.lastname: Banerjee
authors.affiliation: Leesburg Veterinary Internal Medicine , Virginia.
authors.forename: Sybille
authors.initials: S
authors.lastname: Miller
authors.affiliation: University of Washington , Seattle.
authors.forename: Dagmara
authors.initials: D
authors.lastname: Kisiela
authors.affiliation: University of Washington , Seattle.
authors.forename: Evgeni V
authors.initials: EV
authors.lastname: Sokurenko
authors.affiliation: George Washington University , Washington, District of Columbia.
authors.forename: Maliha
authors.initials: M
authors.lastname: Aziz
authors.affiliation: George Washington University , Washington, District of Columbia.
authors.forename: Lance B
authors.initials: LB
authors.lastname: Price
keywords: Escherichia coli infections; ST131; colonization; transmission; whole genome sequence