Biology subjects

Royer, G.

Publications and source records attributed to Royer, G..

9 recordsLinked to original sources

bioRxiv2026

A cellular atlas of Astyanax mexicanus embryogenesis reveals principles of developmental microevolution

The evolution of development is the primary mechanism by which morphological and functional diversity is generated. Comparing the developmental trajectories of single cells in entire embryos across species can reveal how gene expression is conserved and varies, as well as the molecular mechanisms underlying how cell- and tissue-specific changes in developmental regulation generate phenotypic differences. However, this perspective has not addressed the mechanisms of small-scale developmental microevolution, i.e, in closely-related species or even within a single species. The fish Astyanax mexicanus, which comes in two forms adapted to distinct environments - the eyed, river-dwelling morph and the eyeless, cave-adapted morph - is a remarkable model with which to investigate the evolution of gene regulation in a single species. Here, we generated and analyzed a single-nucleus RNA-seq atlas of the development of the two Astyanax morphs, from gastrula to swimming larva. Despite extensive changes in gene expression observed in the eight examined stages, for both ubiquitously-expressed and tissue-specific genes, and in both embryonic and extra-embryonic tissues, the temporal progression of cavefish and surface fish cells was similar in ordinal regression-based pseudotime models using 20-100 core genes. However, transcriptome-wide comparisons of gene expression waves revealed massive heterochronic shifts. In cavefish, some tissues had a majority of genes lagging behind in their transcriptional dynamics (e.g. the optic region), while in others, a majority of genes had accelerated dynamics (e.g. the mesoderm), or else, an equivalent number of genes were found in either category (e.g. the endoderm). Furthermore, cell fate acquisition and differentiation were variably affected in different cavefish lineages, with delays of ~6 hours in the retina, ~2 hours in the axial mesoderm and ~none in the extra-embryonic enveloping layer. Thus, cavefish embryos progress as a mosaic of different tissues, or modules, each following its own transcriptional tempo. Because gene expression differential regulation and time shifts were more prevalent in the early stages and gradually diminished throughout development, we propose that cavefish embryos initially undergo strong decanalisation before becoming re-canalized in line with the shared Astyanax developmental program.

developmental biology↗

bioRxiv2026

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes

ObjectivesModel species are essential for fundamental research in biology. While a complete genomic sequence is a prerequisite for genetic studies, it is not enough on its own. Understanding the three-dimensional organization of the genome is also important, allowing researchers to gain a more realistic understanding of the mechanisms governing genome function. In the fungal model Podospora anserina, although the genomic sequence has been established for a long time, the three-dimensional organization remained unknown. Here we obtained the first Hi-C datasets and present associated 3D models, providing the research community with a valuable resource for better multi-omics data integration. Data descriptionHi-C experiments were performed in duplicate, using nuclei purified from wild-type fungal mycelium. Four FASTQ files were obtained (two per replicate) and used as inputs for the 3DGB workflow with four different output resolutions, to observe the genome organization of P. anserina at different levels of detail (50 kb, 20 kb, 10 kb, and 5 kb). In a context where researchers already have, for this species, a large amount of traditional omics data (ChIP-seq, RNA-seq, etc.), these 3D models are helpful for complementing the linear representation of the genome, which is traditionally used in bioinformatic analyses.

genomics↗

bioRxiv2026

Spatiotemporal dynamics of β-lactam-resistant E. coli in young diseased calves in Wallonia, Belgium

Calves are one of the most common carriers of antibiotic-resistant bacteria among farm animals. However, the impact of antibiotic usage on resistance mechanisms, transmission routes between farms, and the transmission of resistant bacteria to humans remain largely unknown. Here we analyzed the population of {beta}-lactam resistant E. coli isolated over five calving seasons on 444 farms scattered throughout Wallonia, Belgium. Restrictions on critical antibiotics usage led to a reduction of resistance to 3rd generation cephalosporins but has no impact on population structure and {beta}-lactamase genes indicating a resilient population. The correlation between short genetic distances and geographic proximity suggests indirect transmission between farms by fomites with differences between regions east and west of the river Meuse. Phylogenetic analysis of calf isolates with isolates from public databases indicates transitions from bovine to human adaptation. These findings provide new means to further model the spread of E. coli in livestock farming.

microbiology↗

bioRxiv2025

Influence of iron uptake systems on cefiderocol activity in Escherichia coli: at the crossroads of antibiotic resistance and virulence

Cefiderocol (FDC) is a new siderophore-conjugated cephalosporin that enters the periplasm via iron transport systems. However, the specific contribution of individual iron uptake pathways to FDC activity remains unclear. We investigated the role of 12 iron acquisition systems using several Escherichia coli strain collections. FDC MICs were determined in iron-depleted and iron-supplemented media for E. coli mutants (Keio and pathogenic island [PAI]-deleted collections) and for clinical wild-type or TEM-producing E. coli (WT/TEM-Ec) and NDM-producing (NDM-Ec) isolates. The distribution of iron uptake genes was assessed in these isolates. In addition, fec operon prevalence and genomic location were investigated in E. coli genomes from EnteroBase and RefSeq databases. Among Keio and 536-PAI-deleted mutants, only {Delta}cirA and {Delta}fiu (enterobactin system) showed increased FDC MICs (8- and 3-fold, respectively), while {Delta}fecA and {Delta}fecB had lower MICs (3-fold decrease). The fec operon, a known extraintestinal virulence factor, was significantly more prevalent in isolates with FDC MICs above median than in those with MICs below (94% vs. 38% in WT/TEM-Ec; 100% vs. 0% in NDM-Ec). According to EUCAST breakpoints, 66.7% of fec-positive NDM-Ec were resistant to FDC while none of the fec-negative were. The fec operon was found in 46.5% of E. coli genomes, including virulent clones (ST131, 77%) and was mostly chromosome-borne (99%). Plasmid-borne fec closely resembled that of Enterobacter hormaechei, suggesting interspecies transfer. Our findings highlight the role of Fec in reducing FDC susceptibility and promoting resistance in NDM-producing E. coli. They challenge the virulence-resistance trade-off demonstrating the liaisons dangereuses between iron and antibiotics.

microbiology↗

bioRxiv2023

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostics, prevention and treatment is still lacking. We used a collection of 1282 BSI and commensal E. coli isolates collected in France over a 17-year period (2000-2017) and we compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity increased steadily from 23% in 1980 to 46% in 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.

microbiology↗

bioRxiv2022

High pathogenicity island, aer and sit operons: a "menage a trois" in Escherichia coli extra-intestinal virulence

The intrinsic virulence of extra-intestinal pathogenic Escherichia coli is attributed to numerous chromosome and/or plasmid-borne virulence associated genes (VAGs), encoding diverse functions as adhesins, toxins, protectins and iron capture systems, which occur in specific genetic backgrounds. Little is however known on their respective contribution to virulence. Here, by analyzing genomes of 232 sequence type complex (STc) 58 strains, we show that virulence quantified in a mouse model of sepsis emerged in a sub-group of STc58 due to the presence of the siderophore encoding high-pathogenicity island (HPI). When extending our analysis to 370 Escherichia strains we show that full virulence is associated with the presence of the aer or sit operons, in addition to the HPI. The prevalence of these operons, their co-occurrence and genomic location depend on the strain phylogeny. Selection of lineage-dependent specific associations of VAGs argues for strong epistatic interactions shaping the emergence of virulence in E. coli.

microbiology↗

bioRxiv2021

The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections, increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here instead, we whole-genome sequenced a collection of 403 commensal E. coli isolated from fecal samples of healthy adult volunteers in France (1980-2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A) (16.3%), ST73 and ST95 (phylogroup B2) (6.3 and 5.0%, respectively), ST69 (phylogroup D) (4.2%) and ST59 (phylogroup F) (3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine against extra-intestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistances was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independently of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies. IMPORTANCEEscherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an ageing population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance take place. Unfortunately, most whole-genome sequenced strains are isolated from pathogenic conditions. Here, we whole genome sequenced 403 E. coli commensals isolated from healthy French subjects on a 30-year period. Virulence genes increased in frequency by both clonal expansion of clones carrying them and increases in frequency within clones whereas resistance genes increased by within clone increased frequency. Prospective studies of E. coli commensals should be performed worldwide to have a broader picture of evolution and adaptation of this species.

genomics↗

bioRxiv2020

The first AI-based mobile application for antibiotic resistance testing

Antimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. While disk diffusion antibiotic susceptibility testing (AST, also called antibiogram) is broadly used to test for antibiotic resistance in bacterial infections, it faces strong criticism because of inter-operator variability and the complexity of interpretative reading. Automatic reading systems address these issues, but are not always adapted or available to resource-limited settings. We present the first artificial intelligence (AI)-based, offline smartphone application for antibiogram analysis. The application captures images with the phones camera, and the user is guided throughout the analysis on the same device by a user-friendly graphical interface. An embedded expert system validates the coherence of the antibiogram data and provides interpreted results. The fully automatic measurement procedure of our applications reading system achieves an overall agreement of 90% on susceptibility categorization against a hospital-standard automatic system and 98% against manual measurement (gold standard), with reduced inter-operator variability. The applications performance showed that the automatic reading of antibiotic resistance testing is entirely feasible on a smartphone. Moreover our application is suited for resource-limited settings, and therefore has the potential to significantly increase patients access to AST worldwide.

microbiology↗

bioRxiv2018

PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains

Plasmid prediction may be of great interest when studying bacteria such as Enterobacteriaceae. Indeed many resistance and virulence genes are located on such replicons and can have major impact in terms of pathogenicity and spreading capacities. Beyond strains outbreak, plasmids outbreaks have been reported especially for some extended-spectrum beta-lactamase or carbapenemase producing Enterobacteriaceae. Several tools are now available to explore the \"plasmidome\" from whole-genome sequence data, with many interesting and various approaches. However recent benchmarks have highlighted that none of them succeed to combine high sensitivity and specificity. With this in mind we developed PlaScope, a targeted approach to recover plasmidic sequences in Escherichia coli. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, it performs a classification of contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, Plasflow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes containing plasmids. Finally we tested our method on a dataset of E. coli strains exhibiting an elevated rate of extended-spectrum beta-lactamase coding gene chromosomal integration, and we were able to identify 20/21 of these events. Moreover virulence genes and operons predicted locations were also in agreement with the literature. Similar approaches could also be developed for other well-characterized bacteria such as Klebsiella pneumoniae.\n\nData summaryO_LIAll the genomes were downloaded from the National Center for Biotechnology Information Sequence Read Archive and Genome database (Supplementary table 1 and 2).\nC_LIO_LIThe source code of PlaScope is available on Github (https://github.com/GuilhemRoyer/PlaScope).\nC_LI\n\nImportancePlasmid exploration could be of great interest since these replicons are pivotal in the adaptation of bacteria to their environment. They are involved in the exchange of many genes within and between species, with a significant impact on antibiotic resistance and virulence in particular. However, plasmid characterization has been a laborious task for many years, requiring complex conjugation or electroporation manipulations for example. With the advent of whole genome sequencing techniques, access to these sequences is now potentially easier provided that appropriate tools are available. Many softwares have been developed to explore the plasmidome of a large variety of bacteria, but they rarely managed to combine sensitivity and specificity. Here, we focus on a single species, E. coli, and we use the many data available to overcome this problem. With our tool called PlaScope, we achieve high performance compared with two other classifiers, Plasflow and cBar, and we demonstrate the utility of such an approach to determine the location of virulence or resistance genes. We think that PlaScope could be very useful in the analysis of specific and well-known bacteria.

bioinformatics↗