Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss

Authors

Daniel E. Park, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
Maliha Aziz, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
Benjamin J. Koch, Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, 617 S Beaver St., Flagstaff, AZ, 86011, USA.
Kelsey Roach, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
Connie Clabots, Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA.
James R. Johnson, Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA; Department of Medicine, University of Minnesota, 401 East River Parkway, VCRC 1st, UK Floor, Suite 131, Minneapolis, MN, 55455, USA.
Lance B. Price, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
Cindy M. Liu, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA. Electronic address: cindyliu@gwu.edu.

Document Type

Journal Article

Publication Date

12-13-2023

Journal

EBioMedicine

Volume

99

DOI

10.1016/j.ebiom.2023.104909

Keywords

Alistipes; Collinsella; Escherichia coli; Gut microbiome; H30R; ST131

Abstract

BACKGROUND: Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R clade (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. METHODS: Veterans and their household members underwent longitudinal fecal swab surveillance for ST131 in 2014-2018. The fecal microbiome was characterized by 16S rRNA qPCR and sequencing. We evaluated associations between ST131-H30R carriage and gut microbiome at baseline by random forest models to identify the most informative gut bacterial phyla and genera attributes for ST131 and ST131-H30R carriage status. Next, we assessed longitudinal associations between fecal microbiome and ST131-H30R carriage using a mixed-effects logistic regression with longitudinal measures. FINDINGS: Of the 519 participants, 78 were carriers of ST131, among whom 49 had ST131-H30R. At the baseline timepoint, H30R-positive participants had higher proportional abundances of Actinobacteria phylum (mean: 4.9% vs. 3.1%) than ST131-negative participants. H30R-positive participants also had higher abundances of Collinsella (mean: 2.3% vs. 1.1%) and lower abundances of Alistipes (mean: 2.1% vs. 2.6%) than ST131-negative participants. In the longitudinal analysis, Collinsella abundance correlated positively with ST131-H30R carriage status and negatively with the loss of ST131-H30R. Conversely, Alistipes corresponded with the loss and persistent absence of ST131-H30R even in the presence of a household exposure. INTERPRETATION: Abundances of specific fecal bacteria correlated with ST131-H30R carriage, persistence, and loss, suggesting their potential as targets for microbiome-based strategies to reduce carriage of ST131-H30R, a significant risk factor for invasive infections. FUNDING: This work was supported in part by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R21AI117654 and UM1AI104681 and the Office of Research and Development, Department of Veterans Affairs. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Department of Veterans Affairs.

APA Citation

Park, Daniel E.; Aziz, Maliha; Koch, Benjamin J.; Roach, Kelsey; Clabots, Connie; Johnson, James R.; Price, Lance B.; and Liu, Cindy M., "Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss" (2023). GW Authored Works. Paper 3964.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/3964

Department

Environmental and Occupational Health