Biology subjects

El Meouche, I.

Publications and source records attributed to El Meouche, I..

3 recordsLinked to original sources

bioRxiv2025

Exploring mutational possibilities of KPC variants to reach high level resistance to cefiderocol

IntroductionKlebsiella pneumoniae carbapenemase (KPC) is one of the most widespread carbapenemases, with over 242 variants identified. Some, like KPC-33 (D179Y), resist both ceftazidime-avibactam (CZA) and cefiderocol but show only a moderate cefiderocol MIC increase. KPCs success stems from its genetic adaptability, enabling mutation accumulation and necessitating proactive resistance monitoring. This study investigates the mutational possibilities for three KPC variants to develop high-level cefiderocol resistance. MethodUsing random mutagenesis and enrichment selection over a 10-day cefiderocol exposure at increasing concentration, we investigated the mutational potential of KPC-2, KPC-3, and KPC-33 to develop high-level cefiderocol resistance. Resistance mechanisms were then analyzed through phenotypic testing and sequencing. ResultsRandom mutagenesis generated 10, 10, and 105 mutants for blaKPC-2, blaKPC- 3, and blaKPC-33, respectively. After ten days of increasing cefiderocol exposure, MICs rose significantly, with KPC-2 mutants reaching >32 mg/L. Phenotypic analysis revealed a common resistance profile across all tested mutants, with resistance to ceftazidime, ceftazidime-avibactam, cefixime, and piperacillin, but restored susceptibility to carbapenems and most other {beta}-lactams. Sequencing identified key mutations (D179Y- D209V in KPC-2, L169P in KPC-3), while chromosomal changes, particularly cirA and ybiX disruptions, played a crucial role in resistance evolution. DiscussionOur results show that the enriched mutations in KPC genes are not sufficient to confer high cefiderocol MICs, suggesting that, in the studied variants, no simple mutational pathway allows the KPC enzyme to efficiently hydrolyze cefiderocol. These findings underscore the interplay between enzymatic and iron transport mutations in cefiderocol resistance, highlighting the importance of surveillance to anticipate emerging resistance in KPC-producing pathogens.

microbiology↗

bioRxiv2024

Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy

Clostridioides difficile is a gastrointestinal pathogen of both humans and agricultural animals and thus a major One Health threat. The C. difficile species consists of five main clades, with Clade 5 currently undergoing speciation from Clades 1-4. Clade 5 strains are highly prevalent in agricultural animals and can cause zoonotic infections, suggesting that these strains have evolved phenotypes that distinguish them from Clade 1-4 strains. Here, we compare the growth properties of Clade 5 strains to those of Clade 1-4 strains using anaerobic time-lapse microscopy coupled with automated image analysis. Our analyses indicate that Clade 5 strains grow faster and are more likely to form long chains of cells than Clade 1-4 strains. Using comparative genomic and CRISPRi analyses, we show that the chaining phenotype of Clade 5 strains is driven by the orientation of the invertible cmr switch sequence, with chaining strains exhibiting a bias to the cmr-ON state. Interestingly, Clade 5 strains with a bias towards the cmr-ON state shifted to a largely cmr-OFF state during murine infection, suggesting that the cmr-OFF state is under positive selection during infection. Collectively, our data reveal that Clade 5 strains have distinct growth properties, which may allow them to inhabit diverse ecological niches. Author SummaryThe Clade 5 strains of the Clostridioides difficile species are so phylogenetically divergent that they almost meet the threshold of being a distinct species. Although these strains are ubiquitously isolated from agricultural and environmental settings and an important source of zoonotic and community-acquired infections, it is unclear whether they have distinct phenotypic properties that allow them to colonize diverse hosts or persist in the environment. By combining a novel anaerobic time-lapse microscopy method with automated image analysis, we discovered that Clade 5 strains grow faster than strains from other C. difficile clades and that they frequently form long chains. These chaining properties are driven by the environmentally responsive expression of a non-canonical signal transduction system, which our analyses suggest is selected against during murine infection. Collectively, our analyses reveal that Clade 5 strains have distinct growth properties that may promote their persistence in the environment.

microbiology↗

bioRxiv2018

Forecasting when cells die during antibiotic exposure using stochastic gene expression

Antibiotic killing does not occur at a single, precise time for all cells within a population. Variability in time to death can be caused by stochastic expression of genes, resulting in differences in endogenous stress-resistance levels between individual cells in a population. This variability can be part of a bet-hedging strategy where cells leverage noise to ensure a subset of the population can tolerate the drug, while decreasing the overall cost of expressing resistance genes. We asked whether single-cell differences in gene expression prior to antibiotic addition were related to cell survival times after antibiotic exposure for a range of genes of diverse function. We quantified the time to death of single cells under antibiotic exposure in combination with expression of reporters. For some reporters, the time to cell death had a strong relationship with the initial expression level of the genes. Reporters that could forecast cell fate included stress response genes, but also genes involved in a variety of other cellular processes like metabolism. Our results highlight the single-cell level non-uniformity of antibiotic killing and also provide examples of key genes where cell-to-cell variation in expression prior to antibiotic exposure is strongly linked to extended durations of antibiotic survival.

systems biology↗