BSc in Biochemistry & Microbiology, University of Caen, France
MSc in Cellular Biology & Microbiology, University of Caen, France
PhD in Microbiology, University of Caen, France
Post doctoral training with Prof. Jörg Vogel, University of Würzburg, Germany
Post doctoral training with Prof. Sophie Helaine, Imperial College London UK and Harvard Medical School Boston USA
Inserm researcher, U1230 University of Rennes, France
Regulatory RNA Ern0160 controls Enterococcus faecium virulence through direct modulation of expression of LysM domain-containing proteins Loren Dejoies, Valérie Bordeau, Killian Le Neindre, Sophie Reissier, Kevin Arnould, et al. BMC Genomics, 2026 Background Enterococcus faecium is a commensal of the human gut microbiota that can become an opportunistic pathogen, particularly in immunocompromised individuals. Small RNAs (sRNA) are thought to contribute to this shift by enabling rapid bacterial adaptation to environmental changes. Despite this, knowledge of sRNA in E. faecium remains limited. Ern0160, in particular, has attracted interest for its involvement in antibiotic and biocide responses, as well as its role in intestinal colonization in a murine model. Results In this study, we investigated the functions of Ern0160 in E. faecium Aus0004 reference strain and sought to identify its mRNA targets. Transcriptomic and in silico analyses revealed potential regulatory targets, including two homologous genes encoding LysM-containing domain proteins (EFAU004_01059 and EFAU004_01150), both associated with enterococcal pathogenicity. Experimental validation confirmed that increased expression of Ern0160 led to repression of these genes. We further demonstrated direct and specific interactions between Ern0160 and the two homologous target mRNAs. Functional assays in the Galleria mellonella larvae infection model showed that deletion of Ern0160 resulted in increased host mortality, whereas deletion of its targets genes resulted in decreased mortality. These results are consistent with previous findings linking these genes to E. faecium virulence in murine model of systemic and urinary tract infections. Conclusions Our findings suggest that Ern0160 contributes to a regulatory network that modulates E. faecium colonization and infection by targeting genes involved in antimicrobial response and virulence. This study highlights the potential of regulatory RNAs such as Ern0160 to shape the pathogenic behavior of a multi-drug resistant and clinically significant bacterium.
Clinical characteristics, management and outcomes of enterococcal infective endocarditis: an ancillary study from the ESC-EORP EURO-ENDO registry Mary Philip, Robinson Gravier Dumonceau, Rodolfo Citro, Bernard Cosyns, Erwan Donal, et al. European Heart Journal Quality of Care and Clinical Outcomes, 2026 Aims Enterococcal infective endocarditis (EIE) represents a growing proportion of infective endocarditis (IE) cases, particularly among elderly and comorbid patients. EIE poses diagnostic and therapeutic challenges, notably regarding optimal antimicrobial therapy and surgical decision-making. We aimed to compare the clinical characteristics, management, and outcomes of EIE vs. non-enterococcal IE (NEIE) in the ESC-EORP EURO-ENDO registry. Methods and results This ancillary analysis of the prospective EURO-ENDO registry included adult patients with definite or possible IE enrolled between January 2016 and March 2018. Patients with monomicrobial EIE were compared with those with NEIE. Clinical, microbiological, imaging, and therapeutic data were analysed. Multivariable logistic regression including EuroSCORE II and valve status identified independent predictors of in-hospital mortality. Among 3083 patients, 365 (12%) had monomicrobial EIE. Compared with NEIE, EIE patients were older (mean 68 vs. 58 years), had more comorbidities, and more frequent prosthetic valve involvement (41% vs. 26%). Aortic valve localization and colonic uptake on PET/CT were also more common. In-hospital mortality was similar (16% vs. 17%). After adjustment for EuroSCORE II and valve status, EIE was not independently associated with higher in-hospital mortality (adjusted OR 0.67 [95% confidence interval 0.42–1.04]; P = 0.083). Among 195 EIE patients with 1-year follow-up, recurrence occurred in 6%. Healthcare-associated acquisition, prosthetic valve infection, and recurrence were associated with worse outcomes and lower surgical rates. Conclusion EIE affects older, high-risk patients. After adjustment for operative risk, mortality was comparable to other aetiologies, highlighting the need for tailored diagnostic and therapeutic strategies.
Beneficial impact of acquired AmpC β-lactamases on bacterial fitness and pathogenicity: a new paradigm Otávio Hallal Ferreira Raro, Charlotte Michaux, Andrea Endimiani, Jorge Larios, Claudia Aldeia, et al. Mbio, 2026 AmpC-type β-lactamases share structural similarities with penicillin-binding proteins, supporting the view that both enzyme families evolved from a common ancestor. Considering the widespread dissemination of acquired AmpCs in Gram-negative bacteria, we hypothesize that, besides their established role in β-lactam resistance, they may also influence essential bacterial mechanisms. Thus, this study aimed to elucidate whether AmpCs modulate bacterial physiology and fitness. Escherichia coli MG1655 was used as the model organism to assess the impact of clinically relevant acquired AmpCs (CMY, DHA, ACC, and FOX variants) on growth, competition, motility, biofilm formation, and pathogenicity, coupled with transcriptomic profiling. We demonstrated that certain CMY variants (notably CMY-42 and CMY-145) confer an unexpected in vitro growth advantage, whereas CMY-2 enhances pathogenicity in vivo by inducing flagellar production. These findings establish a new paradigm in which some AmpCs act as both resistance determinants and regulators of bacterial fitness and virulence, contributing to the ecological success of Enterobacterales. IMPORTANCE Although β-lactamases have always been considered enzymes involved in resistance to β-lactam antibiotics, they also have to be considered as playing a role in reshaping bacterial physiology. By studying a series of class C β-lactamases, we uncovered an unexpected dual role. Besides conferring resistance to β-lactams, they also impact bacterial growth, motility, and pathogenicity through modulation of flagellar biosynthesis. Strikingly, while CMY-42- and CMY-145-producing recombinant Escherichia coli strains showed enhanced in vitro fitness growth by reducing energy-costly flagellar production, production of CMY-2 (the most commonly identified acquired AmpC β-lactamase identified in Enterobacterales) restored flagella and increased virulence in vivo . This work reframes β-lactamases as metabolic regulators influencing ecological success, offering new insight into how resistance determinants promote the spread and clinical impact of Enterobacterales.
Lactobacillus delbrueckii subsp. allosunkii and lactis as emerging human uropathogens in elderly patients François Guérin, Mohamed Sassi, Francois Gravey, Asma Zouari, Benjamin Quenet, et al. Journal of Clinical Microbiology, 2025 Lactobacillus delbrueckii has been considered a very rare cause of human urinary tract infections (UTIs). However, little is known about its clinical significance and antimicrobial susceptibility, and genomic data from clinical isolates are lacking. This study aimed at analyzing clinical, microbiological, and genomic data of L. delbrueckii urinary isolates. All L. delbrueckii isolates collected from patients hospitalized in a French university hospital from 2014 to 2016 were included. Clinical and biological data were gathered. Species identification was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and MICs were determined using the broth microdilution method. Whole genome sequencing (WGS) was conducted (Illumina MiSeq 2 × 300 bp), and genomes were compared using three approaches (multilocus sequence typing [MLST], average nucleotide identity [ANI], and core genome single nucleotide polymorphism [SNP]). From 2014 to 2016, 48 isolates of L. delbrueckii were recovered from the urine of 48 patients (mean age = 84 years; sex ratio M/F = 0.04). Nearly half (44%) of patients were diagnosed with a UTI, and all had significant cultures (≥10 5 CFU/mL) with a positive direct examination in >90% of cases. The majority of isolates were susceptible to most antibiotics (especially β-lactams), whereas they seemed intrinsically resistant to fosfomycin and metronidazole. Subspecies identification was consistent across the three approaches, showing that most L. delbrueckii isolates belonged to subspecies allosunkii ( n = 40; 83%), followed by subspecies lactis ( n = 8; 17%). Two isolates were resistant to tetracycline (MIC >16 mg/L) and both harbored the tet (W) gene. This study demonstrates the uropathogenic role of L. delbruekii subspecies allosunkii and lactis , particularly in elderly female patients. IMPORTANCE This largest case series of urinary tract infections (UTIs) caused by Lactobacillus delbrueckii clearly demonstrates the uropathogenic role of this species (especially the subspecies allosunkii ) in human UTIs, particularly in elderly female patients and those with underlying comorbidities. This study may change practice in two ways: (i) clinical laboratories, which typically consider lactobacilli from urine samples as contaminants, may need to reassess this practice; (ii) patient care can be improved by prescribing appropriate antibiotics for these underdiagnosed UTIs. L. delbrueckii should be considered an actual pathogen when it is significantly found in the urine of predisposed patients with clinical and/or biological signs of infection. While matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry allows reliable identification of L. delbrueckii , there is also a need for better discrimination between subspecies (especially allosunkii and lactis ). Since L. delbrueckii isolates are usually susceptible to many antibiotics, we recommend β-lactams (especially aminopenicillins) for the treatment of those UTIs.
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives Laura Jenniches, Charlotte Michaux, Linda Popella, Sarah Reichardt, Jörg Vogel, et al. Proceedings of the National Academy of Sciences of the United States of America, 2024 RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3′ untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.
Intoxication of antibiotic persisters by host RNS inactivates their efflux machinery during infection Séverin Ronneau, Charlotte Michaux, Rachel T. Giorgio, Sophie Helaine Plos Pathogens, 2024 The host environment is of critical importance for antibiotic efficacy. By impacting bacterial machineries, stresses encountered by pathogens during infection promote the formation of phenotypic variants that are transiently insensitive to the action of antibiotics. It is assumed that these recalcitrant bacteria—termed persisters—contribute to antibiotic treatment failure and relapsing infections. Recently, we demonstrated that host reactive nitrogen species (RNS) transiently protect persisters against the action of β-lactam antibiotics by delaying their regrowth within host cells. Here, we discovered that RNS intoxication of persisters also collaterally sensitizing them to fluoroquinolones during infection, explaining the higher efficiency of fluoroquinolones against intramacrophage Salmonella. By reducing bacterial respiration and the proton-motive force, RNS inactivate the AcrAB efflux machinery of persisters, facilitating the accumulation of fluoroquinolones intracellularly. Our work shows that target inactivity is not the sole reason for Salmonella persisters to withstand antibiotics during infection, with active efflux being a major contributor to survival. Thus, understanding how the host environment impacts persister physiology is critical to optimize antibiotics efficacy during infection.
Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens Charlotte Michaux, Milan Gerovac, Elisabeth E Hansen, Lars Barquist, Jörg Vogel Microlife, 2023 Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA–protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA–protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA–protein complexes such as the 6S RNA–RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
The RNA-Binding Protein ProQ Promotes Antibiotic Persistence in Salmonella Alisa Rizvanovic, Charlotte Michaux, Margherita Panza, Zeynep Iloglu, Sophie Helaine, et al. Mbio, 2022 Bacteria can avoid eradication by antibiotics through a phenomenon known as persistence. Persister cells arise through phenotypic heterogeneity and constitute a small fraction of dormant cells within a population of actively growing bacteria, which is susceptible to antibiotic killing.
