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Open Forum Infect Dis. 2016 Jun 16;3(3):ofw129. eCollection 2016 Sep.

Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.

Author information

1
Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis.
2
George Washington University , Washington, District of Columbia.
3
Minneapolis Veterans Affairs Health Care System , Minnesota.
4
The Pennsylvania State University , University Park.
5
Children's Hospitals and Clinics of Minnesota , St. Paul.
6
St. Luke's University Hospital and Health Network , Bethlehem, Pennsylvania.
7
University of Missouri , Columbia.
8
Mayo Clinic , Rochester, Minnesota.
9
Leesburg Veterinary Internal Medicine , Virginia.
10
University of Washington , Seattle.

Abstract

Background.  Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence 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 between H30R1 and H30Rx 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 of E coli ST131 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.

KEYWORDS:

Escherichia coli infections; ST131; colonization; transmission; whole genome sequence

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