Investigating the use of bacteriophages as a new decolonization strategy for intestinal carriage of CTX-M-15-producing ST131 Escherichia coli: An in vitro continuous culture system model

Odette J Bernasconi; Edgar I Campos-Madueno; Valentina Donà; Vincent Perreten; Alessandra Carattoli; Andrea Endimiani

doi:10.1016/j.jgar.2020.05.018

Investigating the use of bacteriophages as a new decolonization strategy for intestinal carriage of CTX-M-15-producing ST131 Escherichia coli: An in vitro continuous culture system model

J Glob Antimicrob Resist. 2020 Sep:22:664-671. doi: 10.1016/j.jgar.2020.05.018. Epub 2020 Jun 23.

Authors

Odette J Bernasconi¹, Edgar I Campos-Madueno¹, Valentina Donà², Vincent Perreten³, Alessandra Carattoli⁴, Andrea Endimiani⁵

Affiliations

¹ Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
² Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.
³ Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.
⁴ Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
⁵ Institute for Infectious Diseases, University of Bern, Bern, Switzerland. Electronic address: andrea.endimiani@ifik.unibe.ch.

PMID: 32590187
DOI: 10.1016/j.jgar.2020.05.018

Abstract

Objectives: We investigated the use of bacteriophages as a strategy to decolonize intestinal carriers of multidrug-resistant Escherichia coli.

Methods: A fermentor was used as a continuous culture system for 48h. Two different pools of faeces (studies I and II) obtained from volunteers were spiked with a CTX-M-15-producing ST131 E. coli (strain 4901.28) susceptible to bacteriophages and challenged with three doses of INTESTI Bacteriophage cocktail administered at 2, 6 and 10h after the inoculum. Bacterial typing was performed by implementing microdilution panels, spot test, rep-PCR and whole-genome sequencing (including cgMLST and single-nucleotide variant analysis) obtained using Nanopore and Illumina platforms.

Results: In study I, bacteriophages decreased the numbers of 4901.28 dramatically (≤10¹CFU/mL after 6h). In contrast, during study II, a phage-resistant mutant of 4901.28 persisted in the continuous culture (10⁴CFU/mL at 48h). Whole-genome sequencing revealed the presence of two additional plasmids in the mutant as well as 11 single-nucleotide variants, including one chromosomal in a glycosyltransferase family 2 protein that is responsible for the transfer of sugars to polysaccharides and lipids. In both studies, the commensal E. coli population remained unchanged by the phage treatment maintaining itself at 10⁸CFU/mL.

Conclusions: Our data indicates that bacteriophage cocktails may be implemented to decolonize some intestinal carriers. However, the individual microbiota composition may have an impact on the development of phage resistance. Mechanisms underlying this phenomenon are likely to be various and complex. Further in vivo studies and protein expression experiments are needed to confirm our observations and hypotheses.

Keywords: Bacteriophages; CTX-M-15; Escherichia coli; Gut; Multidrug-resistant; ST131.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages*
Escherichia coli / genetics
Escherichia coli Infections* / prevention & control
Humans
Plasmids
beta-Lactamases / genetics

Substances

beta-Lactamases