Papers by Frederic Veyrier
Pharmaceutics, Oct 26, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Infection through Defective Innate and Resistance to Mycobacterium tuberculosis NOD2-Deficient Mice Have Impaired
Fragment-Based Phenotypic Lead Discovery To Identify New Drug Seeds That Target Infectious Diseases
Fragment-based lead discovery has emerged over the last decades as one of the most powerful techn... more Fragment-based lead discovery has emerged over the last decades as one of the most powerful techniques for identifying starting chemical matter to target specific proteins or nucleic acids in vitro. However, the use of such low-molecular-weight fragment molecules in cell-based phenotypic assays has been historically avoided because of concerns that bioassays would be insufficiently sensitive to detect the limited potency expected for such small molecules and that the high concentrations required would likely implicate undesirable artifacts. Herein, we applied phenotype cell-based screens using a curated fragment library to identify inhibitors against a range of pathogens including Leishmania, Plasmodium falciparum, Neisseria, Mycobacterium, and flaviviruses. This proof-of-concept shows that fragment-based phenotypic lead discovery (FPLD) can serve as a promising complementary approach for tackling infectious diseases and other drug-discovery programs.
Emergence of persistent tubercle bacilli
Nature Microbiology, 2021
PLOS ONE, Jul 30, 2020
The pretreatment of biomass remains a critical requirement for bio-renewable fuel production from... more The pretreatment of biomass remains a critical requirement for bio-renewable fuel production from lignocellulose. Although current processes primarily involve chemical and physical approaches, the biological breakdown of lignin using enzymes and microorganisms is quickly becoming an interesting eco-friendly alternative to classical processes. As a result, bioprospection of wild fungi from naturally occurring lignin-rich sources remains a suitable method to uncover and isolate new species exhibiting ligninolytic activity. In this study, wild species of white rot fungi were collected from Colombian forests based on their natural wood decay ability and high capacity to secrete oxidoreductases with high affinity for phenolic polymers such as lignin. Based on high activity obtained from solid-state fermentation using a lignocellulose source from oil palm as matrix, we describe the isolation and wholegenome sequencing of Dictyopanus pusillus, a wild basidiomycete fungus exhibiting ABTS oxidation as an indication of laccase activity. Functional characterization of a crude enzymatic extract identified laccase activity as the main enzymatic contributor to fungal extracts, an observation supported by the identification of 13 putative genes encoding for homologous laccases in the genome. To the best of our knowledge, this represents the first report of an enzymatic extract exhibiting laccase activity in the Dictyopanus genera, offering means to exploit this species and its enzymes for the delignification process of lignocellulosic by-products from oil palm.
Virulence, 2019
Serine protease autotransporters of Enterobacteriaceae (SPATEs) are secreted proteins that contri... more Serine protease autotransporters of Enterobacteriaceae (SPATEs) are secreted proteins that contribute to virulence and function as proteases, toxins, adhesins, and/or immunomodulators. An extra-intestinal pathogenic E. coli (ExPEC) O1:K1 strain, QT598, isolated from a turkey, was shown to contain vat, tsh, and three uncharacterized SPATE-encoding genes. Uncharacterized SPATEs: Sha (Serine-protease hemagglutinin autotransporter), TagB and TagC (tandem autotransporter genes B and C) were tested for activities including hemagglutination, autoaggregation, and cytotoxicity when expressed in E. coli K-12. Sha and TagB conferred autoaggregation and hemagglutination activities. TagB, TagC, and Sha all exhibited cytopathic effects on a bladder epithelial cell line. In QT598, tagB and tagC are tandemly encoded on a genomic island, and were present in 10% of UTI isolates and 4.7% of avian E. coli. Sha is encoded on a virulence plasmid and was present in 1% of UTI isolates and 20% of avian E. coli. To specifically examine the role of SPATEs for infection, the 5 SPATE genes were deleted from strain QT598 and tested for cytotoxicity. Loss of all five SPATEs abrogated the cytopathic effect on bladder epithelial cells, although derivatives producing any of the 5 SPATEs retained cytopathic activity. In mouse infections, sha gene-expression was up-regulated a mean of sixfold in the bladder compared to growth in vitro. Loss of either tagBC or sha did not reduce urinary tract colonization. Deletion of all 5 SPATEs, however, significantly reduced competitive colonization of the kidney supporting a cumulative role of SPATEs for QT598 in the mouse UTI model.
PLOS Pathogens, Dec 2, 2021
Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic inf... more Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic infectious disease. Leptospirosis is a potentially severe and life-threatening emerging disease with highest burden in subtropical areas and impoverished populations. Mechanisms allowing pathogenic Leptospira to survive inside a host and induce acute leptospirosis are not fully understood. The ability to resist deadly oxidants produced by the host during infection is pivotal for Leptospira virulence. We have previously shown that genes encoding defenses against oxidants in L. interrogans are repressed by PerRA (encoded by LIMLP_10155), a peroxide stress regulator of the Fur family. In this study, we describe the identification and characterization of another putative PerR-like regulator (LIMLP_05620) in L. interrogans. Protein sequence and phylogenetic analyses indicated that LIMLP_05620 displayed all the canonical PerR amino acid residues and is restricted to pathogenic Leptospira clades. We therefore named this PerR-like regulator PerRB. In L. interrogans, the PerRB regulon is distinct from that of PerRA. While a perRA mutant had a greater tolerance to peroxide, inactivating perRB led to a higher tolerance to superoxide, suggesting that these two regulators have a distinct function in the adaptation of L. interrogans to oxidative stress. The concomitant inactivation of perRA and perRB resulted in a higher tolerance to both peroxide and superoxide and, unlike the single mutants, a double perRAperRB mutant was avirulent. Interestingly, this correlated with major changes in gene and non-coding RNA expression. Notably, several virulence-associated genes (clpB, ligA/B, and lvrAB) were repressed. By obtaining a double mutant in a pathogenic Leptospira strain, our study has
Nucleic Acids Research, Nov 9, 2020
In bacteria, DNA methylation can be facilitated by 'orphan' DNA methyltransferases lacking cognat... more In bacteria, DNA methylation can be facilitated by 'orphan' DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
The pretreatment of biomass is a critical requirement of bio-renewable fuel production from ligno... more The pretreatment of biomass is a critical requirement of bio-renewable fuel production from lignocellulose. Although current processes primarily involve chemical and physical approaches, the biological breakdown of lignin using enzymes and microorganisms is quickly becoming an interesting ecofriendly alternative to classical processes. As a result, bioprospection of wild fungi from naturally occurring lignin-rich sources remains a suitable method to uncover and isolate new species exhibiting ligninolytic activity. In this study, wild species of white rot fungi were collected from Colombian forests based on their natural wood decay ability and high capacity to secrete oxidoreductases with high affinity for phenolic polymers such as lignin. Based on high activity obtained from solid-state fermentation using a lignocellulose source from oil palm as matrix, we describe the isolation and whole-genome sequencing of Dictyopanus pusillus, a wild basidiomycete fungus exhibiting ABTS oxidation as an indication of laccase activity. Functional characterization of a crude enzymatic extract identified laccase activity as the main enzymatic contributor to fungal extracts, an observation supported by the identification of 13 putative genes encoding for homologous laccases in the genome. To the best of our knowledge, this represents the first report of an enzymatic extract exhibiting laccase activity in the Dictyopanus genera, offering means to exploit this species and its enzymes for the delignification process of lignocellulosic by-products from oil palm.
Enterohemorragic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen producing shiga toxins (... more Enterohemorragic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen producing shiga toxins (Stx1 and Stx2), can cause hemorrhagic diarrhea, and life-threatening infections. O157:H7 strain EDL933 carries prophages CP-933V and BP-933W that encode shiga toxin genes (stx1 and stx2 respectively). The aim of this work was to investigate the mechanisms of adaptive resistance of EHEC strain EDL933 to a typically “lethal” dose of γ-irradiation (1.5 kGy). Adaptive selection through six passages of exposure to 1.5 kGy resulted in the loss of CP-933V and BP-933W prophages from the genome and mutations within three genes: wrbA, rpoA, and Wt_02639 (molY). Three selected EHEC clones that became irradiation-adapted to the 1.5 kGy dose (C1, C2 and C3) demonstrated increased resistance to oxidative stress, sensitivity to acid pH, and decreased cytotoxicity to Vero cells. To confirm that loss of prophages plays a role in increased radioresistance, C1 and C2 clones were exposed to bacteriophage co...
PLOS Neglected Tropical Diseases, 2021
Background Although Southeast Asia is one of the most leptospirosis afflicted regions, little is ... more Background Although Southeast Asia is one of the most leptospirosis afflicted regions, little is known about the diversity and molecular epidemiology of the causative agents of this widespread and emerging zoonotic disease. Methodology/Principal findings We used whole genome sequencing to examine genetic variation in 75 Leptospira strains isolated from patients in the Lao PDR (Laos) between 2006 and 2017. Eleven serogroups from 4 Leptospira species and 43 cgMLST-defined clonal groups (CGs) were identified. The most prevalent CG was CG272 (n = 18, 26.8%), composed of L. interrogans serogroup Autumnalis isolates. This genotype was recovered throughout the 12-year period and was associated with deaths, and with a large outbreak in neighbouring Thailand. Genome analysis reveals that the CG272 strains form a highly clonal group of strains that have, for yet unknown reasons, recently spread in Laos and Thailand. Additionally, accessory genes clearly discriminate CG272 strains from the oth...
Leptospira ainlahdjerensis sp. nov., Leptospira ainazelensis sp. nov., Leptospira abararensis sp. nov. and Leptospira chreensis sp. nov., four new species isolated from water sources in Algeria
International Journal of Systematic and Evolutionary Microbiology, 2021
Leptospira strains were isolated from freshwater sampled at four sites in Algeria and characteriz... more Leptospira strains were isolated from freshwater sampled at four sites in Algeria and characterized by whole-genome sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The cells were spiral-shaped and motile. Phylogenetic and MALDI-TOF MS analyses showed that the strains can be clearly distinguished from the other described species in the genus Leptospir a, therefore representing two novel species of the pathogen subclade P1 and two novel species of the saprophyte subclade S1. The names Leptospira ainlahdjerensis sp. nov. (type strain 201903070T=KIT0297T=CIP111912T), Leptospira ainazelensis sp. nov. (201903071T=KIT0298T=CIP111913T), Leptospira abararensis sp. nov. (201903074T=KIT0299T=CIP111914T) and Leptospira chreensis (201903075T=KIT0300T=CIP111915T) are proposed.
Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic inf... more Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic infectious disease. Leptospirosis is a potentially severe and life-threatening emerging disease with highest burden in sub-tropical areas and impoverished populations. Mechanisms allowing pathogenic Leptospira to survive inside a host and induce acute leptospirosis are not fully understood. The ability to resist deadly oxidants produced by the host during infection is pivotal for Leptospira virulence. We have previously shown that genes encoding defenses against oxidants in L. interrogans are repressed by PerRA (encoded by LIMLP_10155), a peroxide stress regulator of the Fur family. In this study, we describe the identification and characterization of another putative PerR-like regulator (LIMLP_05620) in L. interrogans. Protein sequence and phylogenetic analyses indicated that LIMLP_05620 displayed all the canonical PerR amino acid residues and is restricted to pathogenic Leptospira clades....
Springer eBooks, 2014
Bacterial cells are encompassed by a macromolecular network of peptidoglycan, the major component... more Bacterial cells are encompassed by a macromolecular network of peptidoglycan, the major component of bacterial cell walls that provides the cell wall strength and determines bacterial morphology. Eukaryotic organisms sense the presence of bacteria by detecting peptidoglycan fragments shed by the bacterium or released through hydrolytic attack by host enzymes. As such, peptidoglycan plays a major role in regulation of host inflammatory homeostasis and has a remarkable variety of influences on the physiological development of the host. This chapter describes the tools necessary to characterize both the biochemistry and biological activity of peptidoglycans purified from a broad range of bacteria. These protocols detail the procedures for purification of peptidoglycan and analysis of its composition by reversed-phase high-performance liquid chromatography (HPLC), taking into account the specific requirements for different types of bacteria, and describe a NF-κBluciferase reporter assay performed using the HEK293T human epithelial cell line, to assess the biological activity of purified peptidoglycans through recognition by mammalian Nod-like receptors Nod1 and Nod2.
Scientific Reports, Nov 12, 2020
Global warming has been associated with increased episodes of mass mortality events in invertebra... more Global warming has been associated with increased episodes of mass mortality events in invertebrates, most notably in bivalves. Although the spread of pathogens is one of multiple factors that contribute to such mass mortality events, we don't fully understand the pathophysiological consequences of sea warming on invertebrates. In this work, we show that in temperature stress conditions, circulating hemocytes in mussels leave the hemolymph to gain access to the intervalvar fluid before being released in seawater. External hemocytes can survive for several hours in seawater before entering other mussels. When infected by bacteria, externally-infected hemocytes can enter naive mussels and promote bacterial dissemination in the host. These results reveal the existence of a new opportunistic mechanism used by pathogens to disseminate in marine ecosystems. Such mechanisms may explain how thermal anomalies triggered by global warming can favor episodic mass mortality observed in recent years in marine ecosystem. Abbreviations A. ater Aulacomya ater M. desolationis Mytilus edulis desolationis M. marinum Mycobacterium marinum IVF Intervalvar fluid Because of their ability to accumulate xenobiotics in their tissues, their wide distribution, and their ecological importance, bivalve mollusks have long been recognized as good biological indicators for monitoring the effects of pollution and global warming in marine habitats 1. They have also been exploited worldwide for their economic and nutritional values. Given their sensitivity to bacterial pathogens and development of different forms of cancer, including horizontally-transmitted leukemia 2,3 , there has been increasing interest in studying the physiology of their immune system, which has until recently received considerably less attention compared to other Metazoans. All living organisms are constantly threatened by surrounding microorganisms seeking to exploit the same environmental niche. This is particularly true for invertebrates living in marine costal ecosystems where concentrations of bacteria are notoriously high. Survival and spread of marine bacteria, however, have to contend with several antagonistic factors including light exposure, nutrient deprivation, and physical and chemical properties of seawater 4 , notwithstanding viruses, which kill 20-40% of marine bacteria on a daily basis 5. When entering into a host, bacteria further face the innate immune response, a crucial first line of host defense against pathogenic microorganisms. In bivalves, elimination of infectious pathogens by the innate immune system involves physical barriers, production of antimicrobial peptides, and phagocytes, which circulate freely in the hemolymph in direct contact with the animal's tissues where they perform local immune surveillance activities 6. Phagocytic cells are also endowed with the ability to move to other compartments if necessary where they remain functionally competent, allowing them to perform a sentinel role similar to leukocytes in vertebrates 7,8. Several studies have further shown that such migration of hemocytes through the pallial (or intervalvar) epithelium is bi-directional 9. Unfortunately, for pathogens that resist phagocytosis or the action of hydrolytic immune mediators, such bidirectional movement provides an ideal gateway for establishing tissue-specific and/or systemic infection in the host 10. This hypothesis is supported by recent studies showing that infection of hemocytes by some pathogens, such as Perkinsus marinus, can upregulate integrin-mediated cell motility of hemocytes, favoring their
Archives of Microbiology
A polyphasic taxonomic approach, incorporating analysis of phenotypic features, cellular fatty ac... more A polyphasic taxonomic approach, incorporating analysis of phenotypic features, cellular fatty acid profiles, 16S rRNA gene sequences, and determination of average nucleotide identity (ANI) plus digital DNA–DNA hybridization (dDDH), was applied to characterize an anaerobic bacterial strain designated KD22T isolated from human feces. 16S rRNA gene-based phylogenetic analysis showed that strain KD22T was found to be most closely related to species of the genus Gabonibacter. At the 16S rRNA gene level, the closest species from the strain KD22T corresponded with Gabonibacter massiliensis GM7T, with a similarity of 97.58%. Cells of strain KD22T were Gram-negative coccobacillus, positive for indole and negative for catalase, nitrate reduction, oxidase, and urease activities. The fatty acid analysis demonstrated the presence of a high concentration of iso-C15: 0 (51.65%). Next, the complete whole-genome sequence of strain KD22T was 3,368,578 bp long with 42 mol% of DNA G + C contents. The ...
Life Science Alliance
Leptospirabacteria comprise numerous species, several of which cause serious disease to a broad r... more Leptospirabacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis–encoding genes reside within the chromosomicrfbgene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of therfbcluster strongly correlates withLeptospiraserovar designation. Whole-genome sequencing of pathogenicL. noguchii, including strains of different serogroups, reveals that therfbcluster undergoes extensive horizontal gene transfer. Therfbclusters from severalLeptospiraspecies disclose a univocal correspondence between gen...
Tractidigestivibacter montrealensis sp. nov., a new member of human gut microbiota isolated from a healthy volunteer
FEMS Microbiology Letters
Strain KD21T, isolated from the fecal sample of a healthy female volunteer, is a strictly anaerob... more Strain KD21T, isolated from the fecal sample of a healthy female volunteer, is a strictly anaerobic, non-motile, Gram-staining-positive, saccharolytic small rod that does not produce spores. Strain KD21T was able to grow in the range of temperature 28°C–37°C (optimum, 37 °C), pH 6.0–8.0 (optimum, pH 7.0), and with 0–5.0 g/l NaCl (optimum, 0 g/l NaCl). Bacteria cells reduced nitrates to nitrites. Its major fatty acids were C18:1ω9c, C16:0, C18:0, and summed in feature 8 (C18:1ω7c and/or C18:1ω6c). 16S rRNA gene phylogenetic analysis revealed that KD21T is a member of the genus Tractidigestivibacter and is distinct from any species with validly published names. The sequence showed 98.48% similarity with T. scatoligenes SK9K4T. The DNA G + C content of strain KD21T was 62.6 mol%. The DNA–DNA hybridization and OrthoANI values between strain KD21T and T. scatoligenes SK9K4T were 40.2% and 90.2%, respectively. Differences in phenotypic, phylogenetic, chemotaxonomic, and genomic characteri...
Cellular adaptation to artificial coccoïd transition
<p>A) A graphical representation of the <i>N</i>. <i>elongata</i> g... more <p>A) A graphical representation of the <i>N</i>. <i>elongata</i> genome sequenced by PacBio is illustrated here using CIRCOS software. The first circle represents the different <i>orf</i> and their orientation. The second circle represents the coverage values (orange) of the Illumina reads obtain by sequencing <i>N</i>. <i>elongata</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> and mapped along the genome of <i>N</i>. <i>elongata</i> wild-type. One can notice the increased coverage by two fold of the DNA region from 0.202 to 0.558 Mbp. Finally, the third internal circle represent the fold change expression, in function of the position, of genes up-regulated (green) and down-regulated (red) of Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> compare to wild type <i>N</i>. <i>elongata</i>. Only genes with a p-value below 0.01 and fold change over 3 are represented. All the fold change values and statistics are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005338#pgen.1005338.s006" target="_blank">S3 Table</a>. B) Verification of transcriptional changes of selected genes, in the different mutants, using rt-PCR and calculated using ΔΔCT (*** p≤0.001; ** p≤0.01; * p≤0.05).</p
Phylogenetic tree based on the 16S rRNA and <i>ppk</i> sequences to evaluate the diversity within the <i>Leptospira</i> genus
<p>In addition to the 16S rRNA sequences from the 64 genomes investigated in the present st... more <p>In addition to the 16S rRNA sequences from the 64 genomes investigated in the present study, those from uncultured strains from the Peruvian Amazon (Clade C) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0007270#pntd.0007270.ref026" target="_blank">26</a>] and from insectivorous bats from eastern China [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0007270#pntd.0007270.ref027" target="_blank">27</a>] were added. The branches are colored according to their belonging to the four main subclades: P1 (red), P2 (purple), S1 (green) and S2 (blue), while the strains of the “clade C” are in black. For the sake of clarity, the bootstrap values are only indicated for the nodes that correspond to the major splits. A tree constructed with the <i>ppk</i> gene sequences is included in the dashed box for comparison. In this case, all bootstrap values less than 100 are indicated at the different nodes.</p
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Papers by Frederic Veyrier