Bacterial predictors of Escherichia coli sequence type 131 colonization and loss

Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R subclone (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. Veterans and their household members underwent longitudinal fecal swab surveillance for ST131, H30R, and H30Rx in 2014-2018. The fecal microbiome was characterized by 16S rRNA real-time PCR and sequencing. Cross-sectional associations between ST131-H30R carriage and gut bacterial phyla and genera were evaluated using chi-squared and Wilcoxon Rank-Sum tests. Associations between genera and longitudinal ST131-H30R carriage were evaluated using mixed effects logistic regression models. Of 519 participants, 78 (15.0%) had ST131, 49 (9.4%) had H30R, and 11 (2.1%) had H30Rx. In cross-sectional analyses, H30R-positive participants exhibited higher proportional abundance compared to ST131-negative participants for the phylum Actinobacteria (mean: 4.9% vs. 3.1%) and genus Collinsella (2.3% vs. 1.1%); the reverse held for the genus Alistipes (means: H30R-positive, 2.1%; ST131-negative, 2.6%). During longitudinal follow-up, Collinsella corresponded with ST131-H30R presence, and decreased in proportional abundance with loss of ST131-H30R. By contrast, Alistipes corresponded with absence of ST131-H30R. Multiple bacterial taxa corresponded with ST131 and ST131-H30R carriage, persistence, and loss, and hence may represent targets for interventions against these important public health threats.