Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis

James R. Johnson, Gregg Davis, Connie Clabots, Brian D. Johnston, Stephen Porter, Chitrita DebRoy, William Pomputius, Peter T. Ender, Michael Cooperstock, Billie Savvas Slater, Ritu Banerjee, Sybille Miller, Dagmara Kisiela, Evgeni V. Sokurenko, Maliha Aziz, Lance B. Price

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberofw129
JournalOpen Forum Infectious Diseases
Volume3
Issue number3
DOIs
StatePublished - Jan 1 2016

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Sequence Analysis
Cluster Analysis
Genome
Escherichia coli
Phylogeny
Pets
Infection
Urinary Tract Infections

All Science Journal Classification (ASJC) codes

  • Oncology
  • Clinical Neurology

Cite this

Johnson, James R. ; Davis, Gregg ; Clabots, Connie ; Johnston, Brian D. ; Porter, Stephen ; DebRoy, Chitrita ; Pomputius, William ; Ender, Peter T. ; Cooperstock, Michael ; Slater, Billie Savvas ; Banerjee, Ritu ; Miller, Sybille ; Kisiela, Dagmara ; Sokurenko, Evgeni V. ; Aziz, Maliha ; Price, Lance B. / Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis. In: Open Forum Infectious Diseases. 2016 ; Vol. 3, No. 3.
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title = "Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis",
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.",
author = "Johnson, {James R.} and Gregg Davis and Connie Clabots and Johnston, {Brian D.} and Stephen Porter and Chitrita DebRoy and William Pomputius and Ender, {Peter T.} and Michael Cooperstock and Slater, {Billie Savvas} and Ritu Banerjee and Sybille Miller and Dagmara Kisiela and Sokurenko, {Evgeni V.} and Maliha Aziz and Price, {Lance B.}",
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Johnson, JR, Davis, G, Clabots, C, Johnston, BD, Porter, S, DebRoy, C, Pomputius, W, Ender, PT, Cooperstock, M, Slater, BS, Banerjee, R, Miller, S, Kisiela, D, Sokurenko, EV, Aziz, M & Price, LB 2016, 'Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis', Open Forum Infectious Diseases, vol. 3, no. 3, ofw129. https://doi.org/10.1093/ofid/ofw129

Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis. / Johnson, James R.; Davis, Gregg; Clabots, Connie; Johnston, Brian D.; Porter, Stephen; DebRoy, Chitrita; Pomputius, William; Ender, Peter T.; Cooperstock, Michael; Slater, Billie Savvas; Banerjee, Ritu; Miller, Sybille; Kisiela, Dagmara; Sokurenko, Evgeni V.; Aziz, Maliha; Price, Lance B.

In: Open Forum Infectious Diseases, Vol. 3, No. 3, ofw129, 01.01.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Household clustering of escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis

AU - Johnson, James R.

AU - Davis, Gregg

AU - Clabots, Connie

AU - Johnston, Brian D.

AU - Porter, Stephen

AU - DebRoy, Chitrita

AU - Pomputius, William

AU - Ender, Peter T.

AU - Cooperstock, Michael

AU - Slater, Billie Savvas

AU - Banerjee, Ritu

AU - Miller, Sybille

AU - Kisiela, Dagmara

AU - Sokurenko, Evgeni V.

AU - Aziz, Maliha

AU - Price, Lance B.

PY - 2016/1/1

Y1 - 2016/1/1

N2 - 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.

AB - 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.

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