The cnf1 gene is associated with an expanding Escherichia coli ST131 H 30Rx/C2 subclade and confers a competitive advantage for gut colonization

Gut Microbes. 2022 Jan-Dec;14(1):2121577. doi: 10.1080/19490976.2022.2121577.

Abstract

Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract and a source of urinary tract pathogens. Bioinformatics analyses of a large collection of E. coli genomes from EnteroBase, enriched in clinical isolates of worldwide origins, suggest the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, is preferentially distributed in four common sequence types (ST) encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment, with known enhanced capacities to colonize the gastrointestinal tract. Statistical projections based on this dataset point to a global expansion of cnf1-positive multidrug-resistant ST131 strains from subclade H30Rx/C2, accounting for a rising prevalence of cnf1-positive strains in ST131. Despite the absence of phylogeographical signals, cnf1-positive isolates segregated into clusters in the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. The suggested dominant expansion of cnf1-positive strains in ST131-H30Rx/C2 led us to uncover the competitive advantage conferred by cnf1 for gut colonization to the clinical strain EC131GY ST131-H30Rx/C2 versus cnf1-deleted isogenic strain. Complementation experiments showed that colon tissue invasion was compromised in the absence of deamidase activity on Rho GTPases by CNF1. Hence, gut colonization factor function of cnf1 was confirmed for another clinical strain ST131-H30Rx/C2. In addition, functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2 and a cnf1-deleted isogenic strain showed no detectable impact of the CNF1 gene on bacterial fitness and inflammation during the acute phase of bladder monoinfection. Together these data argue for an absence of role of CNF1 in virulence during UTI, while enhancing gut colonization capacities of ST131-H30Rx/C2 and suggested expansion of cnf1-positive MDR isolates in subclade ST131-H30Rx/C2.

Keywords: CNF1; Escherichia coli; ExPEC; ST131; UTI; colonization; gastrointestinal tract; rho GTPases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacterial Toxins* / genetics
  • Drug Resistance, Multiple, Bacterial / genetics
  • Escherichia coli
  • Escherichia coli Infections* / microbiology
  • Escherichia coli Proteins* / genetics
  • Gastrointestinal Microbiome*
  • Humans
  • Virulence Factors / genetics
  • beta-Lactamases / genetics
  • beta-Lactamases / metabolism
  • rho GTP-Binding Proteins

Substances

  • Anti-Bacterial Agents
  • Bacterial Toxins
  • Escherichia coli Proteins
  • Virulence Factors
  • cytotoxic necrotizing factor type 1
  • beta-Lactamases
  • rho GTP-Binding Proteins

Grants and funding

This work was supported by Inserm Transversal Programme on Microbiota, the French National Research Agency (ANR-10-LABX-62-IBEID, INCEPTION), ANR-17-CE17-0014 and ANR-21-CE15-0006, the “Fondation ARC” PJA 20191209650, the “Ligue Nationale contre le Cancer Subvention de Recherche Scientifique” RS20/75-63, the “Fondation pour la Recherche Médicale” (Equipe FRM 2016, DEQ20161136698).