Biology subjects

Gaborieau, B.

Publications and source records attributed to Gaborieau, B..

5 recordsLinked to original sources

bioRxiv2024

Phage-phage competition and biofilms reduce the efficacy of a combination of two virulent bacteriophages against Pseudomonas aeruginosa

Combined use of virulent bacteriophages (phages) and antibiotics reduces the severity of difficult-to-treat Pseudomonas aeruginosa infections in many patients. In vitro methods that attempt to reproduce more than one physiological state of the pathogens can provide a valuable assessment of antibacterials like phages. Here, by measuring bacterial killing kinetics and individual replication in different growth conditions, including biofilms and a human lung epithelial cell line, we elucidated factors influencing the efficacy of two virulent phages against P. aeruginosa PAO1. A single administration of phages effectively reduced the P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, however, the emergence of phage-resistant variants occurred subsequently. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem. In contrast, surface-attached biofilms exhibited tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in the antibacterial effect. Moreover, the phage with the shorter lysis time lysed P. aeruginosa more rapidly and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage of the combination. The sequential addition of phages resulted in their unimpeded replication with no increase in bacteriolytic activity. These findings highlight biofilm developmental stages, phage-phage competition, and phage resistance as factors restricting the in vitro efficacy of a two-phage combination. Our findings provide a framework for selecting and optimizing phage combinations for enhanced efficacy against P. aeruginosa, a metabolically flexible pathogen that undergoes specific adaptation within the infected lung.

microbiology↗

bioRxiv2023

Predicting phage-bacteria interactions at the strain level from genomes

Predicting how phages can selectively infect specific bacterial strains holds promise for developing novel approaches to combat bacterial infections and better understanding microbial ecology. Experimental studies on phage-bacteria interactions have been mostly focusing on a few model organisms to understand the molecular mechanisms which makes a particular bacterial strain susceptible to a given phage. However, both bacteria and phages are extremely diverse in natural contexts. How well the concepts learned from well-established experimental models generalize to a broad diversity of what is encountered in the wild is currently unknown. Recent advances in genomics allow to identify traits involved in phage-host specificity, implying that these traits could be utilized for the prediction of such interactions. Here, we show that we could predict outcomes of most phage-bacteria interactions at the strain level in Escherichia natural isolates based solely on genomic data. First, we established a dataset of experimental outcomes of phage-bacteria interactions of 403 natural, phylogenetically diverse, Escherichia strains to 96 bacteriophages matched with fully sequenced and genomically characterized strains and phages. To predict these interactions, we set out to define genomic traits with predictive power. We show that most interactions in our dataset can be explained by adsorption factors as opposed to antiphage systems which play a marginal role. We then trained predictive algorithms to pinpoint which interactions could be accurately predicted and where future research should focus on. Finally, we show the application of such predictions by establishing a pipeline to recommend tailored phage cocktails to target pathogenic strains from their genomes only and show higher efficiency of tailored cocktails on a collection of 100 pathogenic E. coli isolates. Altogether, this work provides quantitative insights into understanding phage-host specificity at the strain level and paves the way for the use of predictive algorithms in phage therapy.

microbiology↗

bioRxiv2022

Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenic Escherichia coli

AO_SCPLOWBSTRACTC_SCPLOWBacteria exposed to killing agents such as antibiotics or viruses develop resistance. While phage therapy, the use of bacteriophages (phages) for treating bacterial infections, is proposed to answer the antibiotic resistance crisis, bacterial resistance to phages remains poorly characterized during phage treatment. We studied a large population of phage-resistant extra-intestinal pathogenic Escherichia coli 536 clones emerging from both in vitro (non-limited liquid medium) and in vivo (murine pneumonia) conditions. Genome sequencing revealed a mutational convergence of phage resistance mechanisms towards the modification of two cell-wall components, the K15 capsule and the LPS, whatever the condition, showing that their identification could be predicted from the in vitro conditions. The fitness cost of all phage resistant clones was broad in terms of growth rate and resistance to grazing by amoeba and could not discriminate K15 capsule to LPS mutants. By contrast, the virulence of the clones tested in mice showed that K15 capsule mutants were as virulent as the wildtype strain while LPS mutants were strongly attenuated. We also found that resistance to one phage led to the sensitization to other phages. In clinics, to control phage-resistant clones that remains virulent phage cocktail should include phages infecting both phage susceptible and future phage resistant clones. ImportanceEscherichia coli is a leading cause of life-threatening infections, including pneumonia acquired during ventilatory assistance for patients hospitalized in Intensive Care Unit, and a major multidrug resistant pathogen. A century-old concept, phage therapy (i.e. using specific anti-bacterial viruses), is being clinically re-evaluated supported with hundreds of successful compassionate phage treatments. However, along billions of years of coevolution bacteria have developed many ways to resist to phages. Phage resistance occurring during phage therapy remains often overlooked despite its critical role for a successful outcome. During this work we characterized phage resistant mutants in a virulent extra-intestinal pathogenic E coli strain and found that (1) phage resistance taking place during a phage treatment in vivo could be predicted from an in vitro assay; (2) phage resistance has, often but not always, a major fitness cost in terms of virulence; and (3) could be countered by appropriate cocktails of phages.

microbiology↗

bioRxiv2022

The selection of antibiotic- and bacteriophage-resistant Pseudomonas aeruginosa is prevented by their combination

ObjectivesBacteria developing resistance compromise the efficacy of antibiotics or bacteriophages (phages). We tested the association of these two antibacterials to circumvent resistance. MethodsWith the Hollow Fiber Infection Model (HFIM), we mimicked the concentration profile of ciprofloxacin in the lungs of patients treated orally for Pseudomonas aeruginosa infections and independently, mimicked a single inhaled administration of phages (one or two phages). ResultsEach treatment selects for antibiotic-or phage-resistant clones in less than 30 h. By contrast, no bacteria were recovered from the HFIM at 72 h when ciprofloxacin was started 4 h post-phage administration, even when increasing the initial bacterial concentration by a 1000 fold. ConclusionThe combination of phages with antibiotics used according to clinical regimens prevents the growth of resistant clones, providing opportunities to downscale the use of multiple antibiotics.

microbiology↗

bioRxiv2021

Combination of in vivo phage therapy data with in silico model highlights key parameters for treatment efficacy

The clinical (re)development of phage therapy to treat antibiotic resistant infections requires grasping specific biological properties of bacteriophages (phages) as antibacterial. However, identification of optimal dosing regimens is hampered by the poor understanding of phage-bacteria interactions in vivo. Here we developed a general strategy coupling in vitro and in vivo experiments with a mathematical model to characterize the interplay between phage and bacterial dynamics during pneumonia induced by a pathogenic strain of Escherichia coli. The model estimates some key parameters for phage therapeutic efficacy, in particular the impact of dose and route of administration on phage dynamics and the synergism of phage and the innate immune response on the bacterial clearance rate. Simulations predict a low impact of the intrinsic phage characteristics in agreement with the current semi-empirical choices of phages for compassionate treatments. Model-based approaches will foster the deployment of future phage therapy clinical trials.

microbiology↗