Intestinal Persistence of Colonizing Escherichia coli Strains, Especially ST131-H30, in Relation to Bacterial and Host Factors

James R. Johnson, Connie Clabots, Stephen B. Porter, Tricia Bender, Brian D. Johnston, Paul Thuras

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Background: Superior gut colonization may underlie the pandemic emergence of the resistance-associated H30 subclone of Escherichia coli sequence type 131 (ST131-H30). Little is known about the associated host and bacterial characteristics, or the comparative persistence of non-ST131 intestinal E. coli. Methods: Generic and fluoroquinolone-resistant E. coli isolates from volunteers' serial fecal samples underwent clonal analysis and extensive polymerase chain reaction (PCR)-based characterization (phylogroup, selected sequence types, virulence genes). Kaplan-Meier survival analysis and Cox proportional hazards survival analysis using penalized regression (a machine-learning method) were used to identify correlates of strain persistence. Results: Screening of 2005 subjects at the Minneapolis VA Medical Center identified 222 subjects (117 veterans, 105 human and animal household members) for longitudinal fecal surveillance. Analysis of their 585 unique-by-subject fecal E. coli strains identified multiple epidemiological, ecological, and bacterial correlates of strain persistence. ST131-H30, a strong univariable correlate of persistence, was superseded in multivariable analysis by outpatient status, fluoroquinolone resistance, and diverse (predominantly iron uptake-related) virulence genes. Conclusions: ST131-H30 exhibits exceptional intestinal persistence, possibly due to a combination of fluoroquinolone resistance and virulence factors, which may be primarily colonization factors. This identifies both likely contributors to the ST131-H30 pandemic and potential targets for interventions against it.

Original languageEnglish (US)
Pages (from-to)2197-2207
Number of pages11
JournalJournal of Infectious Diseases
Issue number12
StatePublished - Jun 15 2022

Bibliographical note

Publisher Copyright:
© 2022 Published by Oxford University Press for the Infectious Diseases Society of America 2022.


  • Escherichia coli
  • ST131
  • ecology
  • fluoroquinolone resistance
  • intestinal colonization
  • machine learning
  • molecular epidemiology
  • multivariable modeling
  • surveillance
  • virulence factors


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