Production

[hal-04197473] Technological developments and 3D imaging for the diagnosis of aquaculture fish diseases

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ano.nymous@ccsd.cnrs.fr.invalid (M. Merhaz) 06 Sep 2023

https://hal.inrae.fr/hal-04197473v1

[hal-04197332] EcoXtract® green solvent increases rainbow trout performances and decreases susceptibility to VHSV

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ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Rigaudeau) 06 Sep 2023

https://hal.inrae.fr/hal-04197332v1

[hal-05095687] Plan de gestion des données de la plateforme d'infectiologie expérimentale des rongeurs et poissons

Plan de gestion de données de la Plateforme d'infectiologie expérimentale des rongeurs et des poissons

ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Rigaudeau) 03 Jun 2025

https://hal.inrae.fr/hal-05095687v1

[hal-03955969] The influences of microbial colonisation and germ-free status on the chicken TCRβ repertoire

Microbial colonisation is paramount to the normal development of the immune system, particularly at mucosal sites. However, the relationships between the microbiome and the adaptive immune repertoire have mostly been explored in rodents and humans. Here, we report a high-throughput sequencing analysis of the chicken TCRβ repertoire and the influences of microbial colonisation on tissue-resident TCRβ+ cells. The results reveal that the microbiome is an important driver of TCRβ diversity in both intestinal tissues and the bursa of Fabricius, but not in the spleen. Of note, public TCRβ sequences (shared across individuals) make a substantial contribution to the repertoire. Additionally, different tissues exhibit biases in terms of their V family and J gene usage, and these effects were influenced by the gut-associated microbiome. TCRβ clonal expansions were identified in both colonised and germ-free birds, but differences between the groups were indicative of an influence of the microbiota. Together, these findings provide an insight into the avian adaptive immune system and the influence of the microbiota on the TCRβ repertoire.

ano.nymous@ccsd.cnrs.fr.invalid (Stefan Dascalu) 25 Jan 2023

https://hal.inrae.fr/hal-03955969v1

[hal-04175372] Differential Salmonella Typhimurium intracellular replication and host cell responses in caecal and ileal organoids derived from chicken

Chicken infection with Salmonella Typhimurium is an important source of foodborne human diseases. Salmonella colonizes the avian intestinal tract and more particularly the caecum, without causing symptoms. This thus poses a challenge for the prevention of foodborne transmission. Until now, studies on the interaction of Salmonella with the avian gut intestine have been limited by the absence of in vitro intestinal culture models. Here, we established intestinal crypt‐derived chicken organoids to better decipher the impact of Salmonella intracellular replication on avian intestinal epithelium. Using a 3D organoid model, we observed a significantly higher replication rate of the intracellular bacteria in caecal organoids than in ileal organoids. Our model thus recreates intracellular environment, allowing Salmonella replication of avian epithelium according to the intestinal segment. Moreover, an inhibition of the cellular proliferation was observed in infected ileal and caecal organoids compared to uninfected organoids. This appears with a higher effect in ileal organoids, as well as a higher cytokine and signaling molecule response in infected ileal organoids at 3 h post-infection (hpi) than in caecal organoids that could explain the lower replication rate of Salmonella observed later at 24 hpi. To conclude, this study demonstrates that the 3D organoid is a model allowing to decipher the intracellular impact of Salmonella on the intestinal epithelium cell response and illustrates the importance of the gut segment used to purify stem cells and derive organoids to specifically study epithelial cell - Salmonella interaction.

ano.nymous@ccsd.cnrs.fr.invalid (Sonia Lacroix-Lamandé) 02 Aug 2023

https://hal.inrae.fr/hal-04175372v1

[hal-04417714] HTLV-1 biofilm polarization maintained by tetraspanin CD82 is required for efficient viral transmission

The human T-lymphotropic virus type 1 (HTLV-1) is an oncogenic retrovirus whose transmission relies primarily on cell-to-cell contacts as cell-free viruses are poorly infectious. Among the intercellular transmission routes described, HTLV-1 biofilms are adhesive structures polarized at the cell surface that confine virions in a protective environment, which is believed to promote their simultaneous delivery during infection. Here, we show that several tetraspanins are enriched in HTLV-1 biofilms and incorporated into the viral envelope. However, we report that only the tetraspanin CD82 interacts with HTLV-1 Gag proteins which initiates their polarization into viral biofilms. Also, we demonstrate that CD82 maintains HTLV-1 biofilm polarization and favors viral transmission, as its silencing induces a complete reorganization of viral clusters at the cell surface and reduces the ability of infected T-cells to transmit the virus. Our results highlight the crucial role of CD82 and its glycosylation state in the architectural organization of HTLV-1 biofilms and their subsequent transfer through intercellular contacts. IMPORTANCE In the early stages of infection, human T-lymphotropic virus type 1 (HTLV-1) dissemination within its host is believed to rely mostly on cell-to-cell contacts. Past studies unveiled a novel mechanism of HTLV-1 intercellular transmission based on the remodeling of the host-cell extracellular matrix and the generation of cell-surface viral assemblies whose structure, composition, and function resemble bacterial biofilms. These polarized aggregates of infectious virions, identified as viral biofilms, allow the bulk delivery of viruses to target cells and may help to protect virions from immune attacks. However, viral biofilms’ molecular and functional description is still in its infancy, although it is crucial to fully decipher retrovirus pathogenesis. Here, we explore the function of cellular tetraspanins (CD9, CD81, CD82) that we detect inside HTLV-1 particles within biofilms. Our results demonstrate specific roles for CD82 in the cell-surface distribution and intercellular transmission of HTLV-1 biofilms, which we document as two essential parameters for efficient viral transmission. At last, our findings indicate that N-glycosylation of cell-surface molecules, including CD82, is required for the polarization of HTLV-1 biofilms and for the efficient transmission of HTLV-1 between T-lymphocytes.

ano.nymous@ccsd.cnrs.fr.invalid (Coline Arone) 25 Jan 2024

https://hal.inrae.fr/hal-04417714v1

[hal-04230480] Tetraspanin CD82 maintains HTLV-1 biofilm polarization and is required for efficient viral transmission

The human T-lymphotropic virus type-1 (HTLV-1) is an oncogenic retrovirus whose transmission relies primarily on cell-to-cell contacts as cell-free viruses are poorly infectious. Among the intercellular transmission routes described, HTLV-1 biofilms are adhesive structures polarized at the cell surface that confine virions in a protective environment, which is believed to promote their simultaneous delivery during infection. Here, we show that several tetraspanins are enriched in HTLV-1 biofilms and incorporated into the viral envelope. However, we report that only tetraspanin CD82 interacts with HTLV-1 Gag which initiates its polarization into viral biofilms. Also, we demonstrate that CD82 maintains HTLV-1 biofilm polarization and favors viral transmission, as its silencing induces a complete reorganization of viral clusters at the cell surface and reduces the ability of infected T-cells to transmit the virus. Our results highlight the crucial role of CD82 in the architectural organization of HTLV-1 biofilms and their transfer through intercellular contacts.

ano.nymous@ccsd.cnrs.fr.invalid (Coline Arone) 06 Oct 2023

https://hal.inrae.fr/hal-04230480v1

[hal-04332121] A pig model of chronic hepatitis E displaying persistent viremia and a downregulation of innate immune responses in the liver

Background: Hepatitis E virus (HEV) is a zoonotic virus transmitted by pig meat and responsible for chronic hepatitis E in immunocompromised patients. It has proved challenging to reproduce this disease in its natural reservoir. We therefore aimed to develop a pig model of chronic hepatitis E to improve the characterization of this disease. Methods: Ten pigs were treated with a tacrolimus-based regimen and intravenously inoculated with HEV. Tacrolimus trough concentration, HEV viremia, viral diversity, innate immune responses, liver histology, clinical disease and biochemical markers were monitored for 11 weeks post-infection (p.i.). Results: HEV viremia persisted for 11 weeks p.i. HEV RNA was detected in the liver, small intestine, and colon at necropsy. Histological analysis revealed liver inflammation and fibrosis. Several mutations selected in the HEV genome were associated with compartmentalization in the feces and intestinal tissues, consistent with the hypothesis of extrahepatic replication in the digestive tract. Antiviral responses were characterized by a downregulation of IFN pathways in the liver, despite an upregulation of RIG-I and ISGs in the blood and liver. Conclusions: We developed a pig model of chronic hepatitis E that reproduced the major hallmarks of this disease. This model revealed a compartmentalization of HEV genomes in the digestive tract and a downregulation of innate immune responses in the liver. These original features highlight the relevance of our model for studies of the pathogenesis of chronic hepatitis E and for validating future treatments.

ano.nymous@ccsd.cnrs.fr.invalid (Nancy León-Janampa) 08 Dec 2023

https://hal.science/hal-04332121v1

[hal-04320097] Caractérisation des particules exhalées par des porcs infectes par un virus influenza porcin

L’objectif principal de ce travail expérimental est la caractérisation physique et biologique des exhalaisons de modèles porcins infectés par un virus influenza porcin. Ces expérimentations sont conduites sur le site de Ploufragan-Plouzané-Niort de l’ANSES dans l’animalerie expérimentale de niveau de biosécurité A3. Un banc expérimental a été développé de manière à pouvoir isoler, collecter et caractériser les émissions respiratoires. La description technique du banc, la procédure expérimentale employée ainsi que des résultats préliminaires de caractérisation physique sont présentés.

ano.nymous@ccsd.cnrs.fr.invalid (Amir Boulbair) 04 Dec 2023

https://u-pec.hal.science/hal-04320097v1

[anses-04123704] Evaluation of early single dose vaccination on swine influenza A virus transmission in piglets: From experimental data to mechanistic modelling

Swine influenza A virus (swIAV) is a major pathogen affecting pigs with a huge economic impact and potentially zoonotic. Epidemiological studies in endemically infected farms permitted to identify critical factors favoring on-farm persistence, among which maternally-derived antibodies (MDAs). Vaccination is commonly practiced in breeding herds and might be used for immunization of growing pigs at weaning. Althoughinterference between MDAs and vaccination was reported in young piglets, its impact on swIAV transmission was not yet quantified. To this aim, this study reports on a transmission experiment in piglets with or without MDAs, vaccinated with a single dose injection at four weeks of age, and challenged 17 days post-vaccination. To transpose small-scale experiments to real-life situation, estimated parameters were used in a simulation tool to assess their influence at the herd level. Based on a thorough follow-up of the infection chain during the experiment, the transmission of the swIAV challenge strain was highly dependent on the MDA status of the pigs when vaccinated. MDA-positive vaccinated animals showed a direct transmission rate 3.6-fold higher than the one obtained in vaccinated animals without MDAs, estimated to 1.2. Vaccination nevertheless reduced significantly the contribution of airborne transmission when compared with previous estimates obtained in unvaccinated animals. The integration of parameter estimates in a large-scale simulation model, representing a typical farrow-to-finish pig herd, evidenced an extended persistence of viral spread when vaccination of sows and single dose vaccination of piglets was hypothesized. When extinction was quasi-systematic at year 5 post-introduction in the absence of sow vaccination but with single dose early vaccination of piglets, the extinction probability fell down to 33% when batch-to-batch vaccination was implemented both in breeding herd and weaned piglets. These results shed light on a potential adverse effect of single dose vaccination in MDA-positive piglets, which might lead to longer persistence of the SwIAV at the herd level.

ano.nymous@ccsd.cnrs.fr.invalid (Mathieu Andraud) 09 Jun 2023

https://anses.hal.science/anses-04123704v1

[hal-04057783] From In Vitro to In Vivo: A Rational Flowchart for the Selection and Characterization of Candidate Probiotic Strains in Intestinal Disorders

Experimental and clinical evidence has demonstrated the potential of probiotic strains in the prevention or treatment of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). However, there is little data on what the methodology leading to the identification of such strains should be. In this work, we propose a new flowchart to identify strains with probiotic potential for the management of IBS and IBD, which we tested on a collection of 39 lactic acid bacteria and Bifidobacteria strains. This flowchart included in vitro tests of immunomodulatory properties on intestinal and peripheral blood mononuclear cells (PBMCs), assessment of the barrier-strengthening effect by measuring transepithelial electric resistance (TEER) and quantification of short-chain fatty acids (SCFAs) and aryl hydrocarbon receptor (AhR) agonists produced by the strains. The in vitro results were then combined in a principal component analysis (PCA) to identify strains associated with an anti-inflammatory profile. To validate our flowchart, we tested the two most promising strains identified in the PCA in mouse models of post-infectious IBS or chemically induced colitis to mimic IBD. Our results show that this screening strategy allows the identification of strains with potential beneficial effects on colonic inflammation and colonic hypersensitivity.

ano.nymous@ccsd.cnrs.fr.invalid (Flore Maillard) 06 Dec 2023

https://uca.hal.science/hal-04057783v1

[hal-04175302] Recombinant viral hemorrhagic septicemia virus with rearranged genomes as vaccine vectors to protect against lethal betanodavirus infection

The outbreaks of viral hemorrhagic septicemia (VHS) and viral encephalopathy and retinopathy (VER) caused by the enveloped novirhabdovirus VHSV, and the non-enveloped betanodavirus nervous necrosis virus (NNV), respectively, represent two of the main viral infectious threats for aquaculture worldwide. Non-segmented negative-strand RNA viruses such as VHSV are subject to a transcription gradient dictated by the order of the genes in their genomes. With the goal of developing a bivalent vaccine against VHSV and NNV infection, the genome of VHSV has been engineered to modify the gene order and to introduce an expression cassette encoding the major protective antigen domain of NNV capsid protein. The NNV Linker-P specific domain was duplicated and fused to the signal peptide (SP) and the transmembrane domain (TM) derived from novirhabdovirus glycoprotein to obtain expression of antigen at the surface of infected cells and its incorporation into viral particles. By reverse genetics, eight recombinant VHSVs (rVHSV), termed NxGyCz according to the respective positions of the genes encoding the nucleoprotein (N) and glycoprotein (G) as well as the expression cassette (C) along the genome, have been successfully recovered. All rVHSVs have been fully characterized in vitro for NNV epitope expression in fish cells and incorporation into VHSV virions. Safety, immunogenicity and protective efficacy of rVHSVs has been tested in vivo in trout ( Oncorhynchus mykiss) and sole ( Solea senegalensis ). Following bath immersion administration of the various rVHSVs to juvenile trout, some of the rVHSVs were attenuated and protective against a lethal VHSV challenge. Results indicate that rVHSV N2G1C4 is safe and protective against VHSV challenge in trout. In parallel, juvenile sole were injected with rVHSVs and challenged with NNV. The rVHSV N2G1C4 is also safe, immunogenic and efficiently protects sole against a lethal NNV challenge, thus presenting a promising starting point for the development of a bivalent live attenuated vaccine candidate for the protection of these two commercially valuable fish species against two major diseases in aquaculture.

ano.nymous@ccsd.cnrs.fr.invalid (Sandra Souto) 02 Aug 2023

https://hal.inrae.fr/hal-04175302v1

[hal-04177128] Staphylococcus epidermidis isolates from atopic or healthy skin have opposite effect on skin cells: potential implication of the AHR pathway modulation

Introduction S taphylococcus epidermidis is a commensal bacterium ubiquitously present on human skin. This species is considered as a key member of the healthy skin microbiota, involved in the defense against pathogens, modulating the immune system, and involved in wound repair. Simultaneously, S. epidermidis is the second cause of nosocomial infections and an overgrowth of S. epidermidis has been described in skin disorders such as atopic dermatitis. Diverse isolates of S. epidermidis co-exist on the skin. Elucidating the genetic and phenotypic specificities of these species in skin health and disease is key to better understand their role in various skin conditions. Additionally, the exact mechanisms by which commensals interact with host cells is partially understood. We hypothesized that S. epidermidis isolates identified from different skin origins could play distinct roles on skin differentiation and that these effects could be mediated by the aryl hydrocarbon receptor (AhR) pathway. Methods For this purpose, a library of 12 strains originated from healthy skin (non-hyperseborrheic (NH) and hyperseborrheic (H) skin types) and disease skin (atopic (AD) skin type) was characterized at the genomic and phenotypic levels. Results and discussion Here we showed that strains from atopic lesional skin alter the epidermis structure of a 3D reconstructed skin model whereas strains from NH healthy skin do not. All strains from NH healthy skin induced AhR/OVOL1 path and produced high quantities of indole metabolites in co-culture with NHEK; especially indole-3-aldehyde (IAld) and indole-3-lactic acid (ILA); while AD strains did not induce AhR/OVOL1 path but its inhibitor STAT6 and produced the lowest levels of indoles as compared to the other strains. As a consequence, strains from AD skin altered the differentiation markers FLG and DSG1. The results presented here, on a library of 12 strains, showed that S. epidermidis originated from NH healthy skin and atopic skin have opposite effects on the epidermal cohesion and structure and that these differences could be linked to their capacity to produce metabolites, which in turn could activate AHR pathway. Our results on a specific library of strains provide new insights into how S. epidermidis may interact with the skin to promote health or disease.

ano.nymous@ccsd.cnrs.fr.invalid (Leslie Landemaine) 04 Aug 2023

https://hal.inrae.fr/hal-04177128v1

[hal-04189068] Modulation of gut microbiota by antibiotics did not affect anhedonia in a high-fat diet-induced model of depression in male mice

Background: Long-term consumption of a high-fat diet (HFD) causes obesity and is a risk factor for depression. The HFD has a significant impact on the gut microbiota, and dysbiosis of the microbiota is now associated with certain psychiatric disorders such as anxiety and depression. We aimed to investigate whether modulation by antibiotic treatment of the composition of the gut microbiota in diet-induced obese (DIO) C57BL/6J male mice has an impact on depressive-like behaviour. Methods: In this study, we have analysed the effects of a 15 weeks HFD on helplessness assessed in the forced swim test and anhedonia assessed in the sucrose preference test. Two weeks before the start of the behavioural tests, a group of HFD mice were given a combination of two non-absorbable antibiotics, neomycin and polymyxin B. Results: In DIO mice, anhedonia and significant changes in the composition of the gut microbiota at the phyla and family level were observed. On the other hand, there was no significant effect of HFD on the peripheral inflammatory profile. In DIO mice, antibiotic treatment resulted in very pronounced alteration in the composition of the gut microbiota, without any change in anhedonia behaviour. Conclusion: In DIO mice, only four families of bacteria were not affected in their relative abundance by the antibiotic treatment, the Bifidobacteriaceae, Erysipelotrichaceae, Rikenellaceae and Streptococcaceae. This stability concomitant with that of anhedonia suggests that these families may be involved in anhedonia in DIO mice.

ano.nymous@ccsd.cnrs.fr.invalid (Magali Monnoye) 28 Aug 2023

https://hal.inrae.fr/hal-04189068v1

[hal-04172440] Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

Antiviral innate immunity is orchestrated by the interferon system, which appeared in ancestors of jawed vertebrates. Interferon upregulation induces hundreds of interferon-stimulated-genes (ISGs) with effector or regulatory functions. Here we investigated the evolutionary diversification of ISG responses through comparison of two salmonid fishes, accounting for the impact of sequential whole genome duplications ancestral to teleosts and salmonids. We analysed the transcriptomic response of the IFN pathway in the head kidney of rainbow trout and Atlantic salmon, which separated 25-30 Mya. We identified a large set of ISGs conserved in both species and cross-referenced them with zebrafish and human ISGs. In contrast, around one-third of salmonid ISG lacked orthologs in human, mouse, chicken or frog, and often between rainbow trout and Atlantic salmon, revealing a fast-evolving, lineage-specific arm of the antiviral response. This study also provides a key resource for in-depth functional analysis of ISGs in salmonids of commercial significance.

ano.nymous@ccsd.cnrs.fr.invalid (Thomas C Clark) 27 Jul 2023

https://hal.inrae.fr/hal-04172440v1

[hal-04344510] Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery

Background Most interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother–offspring transmission of microorganisms is the most important factor influencing microbial colonization in mammals, and C-section delivery (CSD) is an important disruptive factor of this transfer. Recently, the deregulation of symbiotic host-microbe interactions in early life has been shown to alter the maturation of the immune system, predisposing the host to gut barrier dysfunction and inflammation. The main goal of this study is to decipher the role of the early-life gut microbiota-barrier alterations and its links with later-life risks of intestinal inflammation in a murine model of CSD. Results The higher sensitivity to chemically induced inflammation in CSD mice is related to excessive exposure to a too diverse microbiota too early in life. This early microbial stimulus has short-term consequences on the host homeostasis. It switches the pup’s immune response to an inflammatory context and alters the epithelium structure and the mucus-producing cells, disrupting gut homeostasis. This presence of a too diverse microbiota in the very early life involves a disproportionate short-chain fatty acids ratio and an excessive antigen exposure across the vulnerable gut barrier in the first days of life, before the gut closure. Besides, as shown by microbiota transfer experiments, the microbiota is causal in the high sensitivity of CSD mice to chemical-induced colitis and in most of the phenotypical parameters found altered in early life. Finally, supplementation with lactobacilli, the main bacterial group impacted by CSD in mice, reverts the higher sensitivity to inflammation in ex-germ-free mice colonized by CSD pups’ microbiota. Conclusions Early-life gut microbiota-host crosstalk alterations related to CSD could be the linchpin behind the phenotypic effects that lead to increased susceptibility to an induced inflammation later in life in mice.

ano.nymous@ccsd.cnrs.fr.invalid (M. Barone) 30 May 2024

https://hal.inrae.fr/hal-04344510v1

[hal-04271263] Non-Steroidal Estrogens Inhibit Influenza Virus by Interacting with Hemagglutinin and Preventing Viral Fusion

Influenza virus is one of the main causes of respiratory infections worldwide. Despite the availability of seasonal vaccines and antivirals, influenza virus infections cause an important health and economic burden. Therefore, the need to identify alternative antiviral strategies persists. In this study, we identified non-steroidal estrogens as potent inhibitors of influenza virus due to their interaction with the hemagglutinin protein, preventing viral entry. This activity is maintained in vitro, ex vivo, and in vivo. Therefore, we found a new domain to target on the hemagglutinin and a class of compounds that could be further optimized for influenza treatment.

ano.nymous@ccsd.cnrs.fr.invalid (Elisa Franzi) 10 Nov 2023

https://hal.science/hal-04271263v1

[hal-04229569] The Smallest Infectious Substructure Encoding the Prion Strain Structural Determinant Revealed by Spontaneous Dissociation of Misfolded Prion Protein Assemblies

It is commonly accepted that the prion replicative propensity and strain structural determinant (SSD) are encoded in the fold of PrPSc amyloid fibril assemblies. By exploring the quaternary structure dynamicity of several prion strains, we revealed that all mammalian prion assemblies exhibit the generic property of spontaneously generating two sets of discreet infectious tetrameric and dimeric species differing significantly by their specific infectivity. By using perturbation approaches such as dilution and ionic strength variation, we demonstrated that these two oligomeric species were highly dynamic and evolved differently in the presence of chaotropic agents. In general, our observations of seven different prion strains from three distinct species highlight the high dynamicity of PrPSc assemblies as a common and intrinsic property of mammalian prions. The existence of such small infectious PrPSc species harboring the SSD indicates that the prion infectivity and the SSD are not restricted only to the amyloid fold but can also be encoded in other alternative quaternary structures. Such diversity in the quaternary structure of prion assemblies tends to indicate that the structure of PrPSc can be divided into two independent folding domains: a domain encoding the strain structural determinant and a second domain whose fold determines the type of quaternary structure that could adopt PrPSc assemblies.

ano.nymous@ccsd.cnrs.fr.invalid (Jan Bohl) 23 Oct 2023

https://hal.science/hal-04229569v1

[hal-04107725] Investigation of the Genus Flavobacterium as a Reservoir for Fish-Pathogenic Bacterial Species: the Case of Flavobacterium collinsii

Bacteria of the genus Flavobacterium are recovered from a large variety of environments. Among the described species, Flavobacterium psychrophilum and Flavobacterium columnare cause considerable losses in fish farms. Alongside these well-known fish-pathogenic species, isolates belonging to the same genus recovered from diseased or apparently healthy wild, feral, and farmed fish have been suspected to be pathogenic. Here, we report the identification and genomic characterization of a Flavobacterium collinsii isolate (TRV642) retrieved from rainbow trout spleen. A phylogenetic tree of the genus built by aligning the core genome of 195 Flavobacterium species revealed that F. collinsii stands within a cluster of species associated with diseased fish, the closest one being F. tructae, which was recently confirmed as pathogenic. We evaluated the pathogenicity of F. collinsii TRV642 as well as of Flavobacterium bernardetii F-372T, another recently described species reported as a possible emerging pathogen. Following intramuscular injection challenges in rainbow trout, no clinical signs or mortalities were observed with F. bernardetii. F. collinsii showed very low virulence but was isolated from the internal organs of survivors, indicating that the bacterium is able to survive inside the host and may provoke disease in fish under compromised conditions such as stress and/or wounds. Our results suggest that members of a phylogenetic cluster of fish-associated Flavobacterium species may be opportunistic fish pathogens causing disease under specific circumstances. IMPORTANCE Aquaculture has expanded significantly worldwide in the last decades and accounts for half of human fish consumption. However, infectious fish diseases are a major bottleneck for its sustainable development, and an increasing number of bacterial species from diseased fish raise a great concern. The current study revealed phylogenetic associations with ecological niches among the Flavobacterium species. We also focused on Flavobacterium collinsii, which belongs to a group of putative pathogenic species. The genome contents revealed a versatile metabolic repertoire suggesting the use of diverse nutrient sources, a characteristic of saprophytic or commensal bacteria. In a rainbow trout experimental challenge, the bacterium survived inside the host, likely escaping clearance by the immune system but without provoking massive mortality, suggesting opportunistic pathogenic behavior. This study highlights the importance of experimentally evaluating the pathogenicity of the numerous bacterial species retrieved from diseased fis

ano.nymous@ccsd.cnrs.fr.invalid (Bo-Hyung Lee) 05 Jun 2023

https://hal.science/hal-04107725v1

[hal-04176764] Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to Cold Water Disease

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused by Flavobacterium psychrophilum represents a major threat for freshwater salmonid farming worldwide. A collection of rainbow trout (Oncorhynchus mykiss) isogenic lines was previously produced from a French domestic population. Here, we compared BCWD resistance phenotypes using a subset of isogenic lines chosen for their contrasted susceptibilities to F. psychrophilum. We applied individual monitoring to document the infection process, including time-course quantification of bacteremia and innate immune response. Strikingly, BCWD resistance was correlated with a lower bacterial growth rate in blood. Several immune genes were expressed at higher levels in resistant fish regardless of infection: the Type II arginase (arg2), a marker for M2 macrophages involved in anti-inflammatory responses and tissue repair, and two Toll-like receptors (tlr2/tlr7), responsible for pathogen detection and inflammatory responses. This study highlights the importance of innate and intrinsic defense mechanisms in determining the outcome of F. psychrophilum infections, and illustrates that non-lethal time-course blood sampling for individual monitoring of bacteremia is a powerful tool to resolve within-host pathogen behavior in bacterial fish diseases.

ano.nymous@ccsd.cnrs.fr.invalid (Bo-Hyung Lee) 01 Oct 2025

https://hal.inrae.fr/hal-04176764v1

[hal-04172998] Deficiency in hereditary hemorrhagic telangiectasia-associated Endoglin elicits hypoxia-driven heart failure in zebrafish

Hereditary hemorrhagic telangiectasia (HHT) is a rare genetic disease caused by mutations affecting components of bone morphogenetic protein (BMP)/transforming growth factor-β (TGF-β) signaling in endothelial cells. This disorder is characterized by arteriovenous malformations that are prone to rupture, and the ensuing hemorrhages are responsible for iron-deficiency anemia. Along with activin receptor-like kinase (ALK1), mutations in endoglin are associated with the vast majority of HHT cases. In this study, we characterized the zebrafish endoglin locus and demonstrated that it produces two phylogenetically conserved protein isoforms. Functional analysis of a CRISPR/Cas9 zebrafish endoglin mutant revealed that Endoglin deficiency is lethal during the course from juvenile stage to adulthood. Endoglin-deficient zebrafish develop cardiomegaly, resulting in heart failure and hypochromic anemia, which both stem from chronic hypoxia. endoglin mutant zebrafish display structural alterations of the developing gills and underlying vascular network that coincide with hypoxia. Finally, phenylhydrazine treatment demonstrated that lowering hematocrit/blood viscosity alleviates heart failure and enhances the survival of Endoglin-deficient fish. Overall, our data link Endoglin deficiency to heart failure and establish zebrafish as a valuable HHT model.

ano.nymous@ccsd.cnrs.fr.invalid (Etienne Lelièvre) 21 May 2024

https://hal.inrae.fr/hal-04172998v1

[hal-04116796] DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part II – the impact of lactation rank

Mastitis is among the main reasons women cease breastfeeding. In farm animals, mastitis results in significant economic losses and the premature culling of some animals. Nevertheless, the effect of inflammation on the mammary gland is not completely understood. This article discusses the changes to DNA methylation in mouse mammary tissue caused by lipopolysaccharide-induced inflammation after in vivo intramammary challenges and the differences in DNA methylation between 1st and 2nd lactations. Lactation rank induces 981 differential methylations of cytosines (DMCs) in mammary tissue. Inflammation in 1st lactation compared to inflammation in 2nd lactation results in the identification of 964 DMCs. When comparing inflammation in 1st vs. 2nd lactations with previous inflammation history, 2590 DMCs were identified. Moreover, Fluidigm PCR data show changes in the expression of several genes related to mammary function, epigenetic regulation, and the immune response. We show that the epigenetic regulation of two successive physiological lactations is not the same in terms of DNA methylation and that the effect of lactation rank on DNA methylation is stronger than that of the onset of inflammation. The conditions presented here show that few DMCs are shared between comparisons, suggesting a specific epigenetic response depending on lactation rank, the presence of inflammation, and even whether the cells had previously suffered inflammation. In the long term, this information could lead to a better understanding of the epigenetic regulation of lactation in both physiological and pathological conditions.

ano.nymous@ccsd.cnrs.fr.invalid (E Ivanova) 05 Jun 2023

https://hal.inrae.fr/hal-04116796v1

[hal-04127637] DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part I – the impact of inflammation

Mastitis is among the main reasons women cease breastfeeding, which leads to them supplementing breast milk with artificial formula. In farm animals, mastitis results in significant economic losses and the premature culling of some animals. Nevertheless, researchers do not know enough about the effect of inflammation on the mammary gland. This article discusses the changes to DNA methylation in mouse mammary tissue caused by lipopolysaccharide-induced inflammation (4 h post-injection of lipopolysaccharide). We analysed the expression of some genes related to mammary gland function, epigenetic regulation, and the immune response. The analysis focused on three comparisons: inflammation during the first lactation, inflammation during second lactation with no history of inflammation, and inflammation during second lactation with previous inflammation. We identified differentially methylated cytosines (DMCs), differentially methylated regions (DMRs), and some differentially expressed genes (DEGs) for each comparison. The three comparisons shared some DEGs; however, few DMCs and only one DMR were shared. These observations suggest that inflammation is one of several factors affecting epigenetic regulation during successive lactations. Furthermore, the comparison between animals in second lactation with and without inflammation, with no inflammation history during first lactation showed a different pattern compared to the other conditions in this experiment. This indicates that inflammation history plays an important role in determining epigenetic changes. The data presented in this study suggest that lactation rank and previous inflammation history are equally important when explaining mammary tissue gene expression and DNA methylation changes.

ano.nymous@ccsd.cnrs.fr.invalid (E. Ivanova) 14 Jun 2023

https://hal.inrae.fr/hal-04127637v1

[hal-04294675] Identification of a pharyngeal mucosal lymphoid organ in zebrafish and other teleosts: Tonsils in fish?

The constant exposure of the fish branchial cavity to aquatic pathogens causes local mucosal immune responses to be extremely important for their survival. Here, we used a marker for T lymphocytes/natural killer (NK) cells (ZAP70) and advanced imaging techniques to investigate the lymphoid architecture of the zebrafish branchial cavity. We identified a sub-pharyngeal lymphoid organ, which we tentatively named "Nemausean lymphoid organ" (NELO). NELO is enriched in T/NK cells, plasma/B cells, and antigen-presenting cells embedded in a network of reticulated epithelial cells. The presence of activated T cells and lymphocyte proliferation, but not V(D)J recombination or hematopoiesis, suggests that NELO is a secondary lymphoid organ. In response to infection, NELO displays structural changes including the formation of T/NK cell clusters. NELO and gill lymphoid tissues form a cohesive unit within a large mucosal lymphoid network. Collectively, we reveal an unreported mucosal lymphoid organ reminiscent of mammalian tonsils that evolved in multiple teleost fish familie

ano.nymous@ccsd.cnrs.fr.invalid (Julien Resseguier) 27 May 2025

https://hal.science/hal-04294675v1

[hal-03943007] An Isolate of Streptococcus mitis Displayed In Vitro Antimicrobial Activity and Deleterious Effect in a Preclinical Model of Lung Infection

Microbiota studies have dramatically increased over these last two decades, and the repertoire of microorganisms with potential health benefits has been considerably enlarged. The development of next generation probiotics from new bacterial candidates is a long-term strategy that may be more efficient and rapid with discriminative in vitro tests. Streptococcus strains have received attention regarding their antimicrobial potential against pathogens of the upper and, more recently, the lower respiratory tracts. Pathogenic bacterial strains, such as non-typable Haemophilus influenzae (NTHi), Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus), are commonly associated with acute and chronic respiratory diseases, and it could be interesting to fight against pathogens with probiotics. In this study, we show that a Streptococcus mitis (S. mitis) EM-371 strain, isolated from the buccal cavity of a human newborn and previously selected for promising anti-inflammatory effects, displayed in vitro antimicrobial activity against NTHi, P. aeruginosa or S. aureus. However, the anti-pathogenic in vitro activity was not sufficient to predict an efficient protective effect in a preclinical model. Two weeks of treatment with S. mitis EM-371 did not protect against, and even exacerbated, NTHi lung infection.

ano.nymous@ccsd.cnrs.fr.invalid (Elliot Mathieu) 06 Dec 2023

https://hal.science/hal-03943007v1

[anses-04228409] Controlled Experimental Infection in Pigs with a Strain of Yersinia enterocolitica Harboring Genetic Markers for Human Pathogenicity: Colonization and Stability

Yersinia enterocolitica (Ye) is one of the major causes of foodborne zoonosis. The BT4/O:3 bioserotype is most commonly isolated in human infections. Pigs are considered the main reservoir of Ye, and hence, understanding the dynamics of infection by this pathogen at the individual and group levels is crucial. In the present study, an experimental model was validated in Large White pigs infected with a BT4/O:3 strain. This study showed that Ye contamination in pigs may occur via the introduction of the bacteria not only by mouth but also by snout, with a colonization process consisting of three periods corresponding to three contamination statuses of pigs: P1, corresponding to the 24 h following ingestion or inhalation of Ye with the appearance of bacteria in tonsils or in feces; P2, from 2 days postinoculation (dpi), corresponding to expansion of Ye and colonization of the digestive system and extraintestinal organs associated with an IgG serological response; and P3, after 21 dpi, corresponding to regression of colonization with intermittent Ye detection in tonsils and feces. Although the inoculated strain persisted up to 56 dpi in all pigs, genetic variations with the loss of the gene yadA (a gene involved in human infection) and the emergence of two new multilocus variable-number tandemrepeat analysis (MLVA) profiles were observed in 33% of the 30 isolates studied. This experimental infection model of pigs by Ye provides new insights into the colonization steps in pigs in terms of bacterial distribution over time and bacterial genetic stability.

ano.nymous@ccsd.cnrs.fr.invalid (Emilie Esnault) 04 Oct 2023

https://anses.hal.science/anses-04228409v1

[anses-04040798] Research Note: Analysis of immune responses in broilers after vaccination against Campylobacter jejuni

Campylobacter infections traced mainly to poultry products are major bacterial foodborne zoonoses. Among the many control strategies evaluated at primary poultry level to reduce these infections, vaccination could be a solution, but no effective vaccines are available to date. A better understanding of the immune mechanisms involved in protection against Campylobacter would be helpful for designing novel vaccine strategies. The present study was designed to analyze in more depth the immune responses developed in broilers in order to potentially identify which immune parameters may be important for establishing protection against Campylobacter by comparing the immune responses obtained here with those obtained in a previous study performed on vaccinated specific-pathogen-free Leghorn chickens that presented a partial reduction of Campylobacter after experimental challenge. The protection against Campylobacter colonization was evaluated at different time points over 40 d of rearing, by measuring specific IgY levels in serum and IgA antibodies in bile reflecting the systemic and mucosal humoral responses respectively and the relative expressions of 9 cecal immune marker genes (cytokines and antimicrobial peptides), which reflect the innate and cellular immune responses. Despite no reduction of Campylobacter in the cecum, a systemic immune response over time characterized by the production of specific anti-flagellin IgY was observed, in addition to upregulation of the antimicrobial peptide avian b-defensin (AvBD) 12 gene expression in the cecum of vaccinated broilers compared with the placebo group. However, the levels of specific anti-flagellin mucosal IgA antibodies in the bile as well as the relative expression of other cecal cytokines studied was underexpressed in the vaccinated group or similar in both groups.

ano.nymous@ccsd.cnrs.fr.invalid (Noémie Gloanec) 22 Mar 2023

https://anses.hal.science/anses-04040798v1

[hal-04174029] Flying syringes for emerging enzootic virus screening: proof of concept for the devlopment of noninvasive xenosurveillance tools based on Tsetse flies

Pathogen transfers between wild and domestic animals and between animals and humans are increasing. Their dramatic consequences for public and veterinary health as well as for conservation call for innovative and user-friendly methods for pathogen surveillance in wildlife. Xenosurveillance, a method based on the use of invertebrates (e.g., mosquitoes, hematophagous flies, leeches, cadaveric arthropods) to sample animal tissues (e.g., blood) and the associated pathogens, is one of these tools. Previously, we demonstrated that hematophagous flies, such as tsetse flies, could be useful to detect and identify the etiological agents of malaria in a diverse range of mammals in Gabon. However, we did not assess whether this method can be also used to detect viruses. In the present study, we experimentally fed tsetse flies (Glossina fuscipes fuscipes) rabbit blood containing different viruses of medical or veterinary importance (Zika, Dengue, Chikungunya, African swine fever, Bluetongue, and peste des petits ruminants viruses). Then, we used quantitative PCR (i) to determine for how long viral nucleic acid fragments remained detectable in the tsetse midgut during blood digestion and (ii) to compare two blood meal preservation methods (i.e., FTA cards and RNAlater solution) tested using tsetse flies engorged with blood and dengue-2 virus. All viruses remained detectable for 6 days after feeding, although the detection probability significantly decreased over time. FTA cards and RNAlater solution gave similar results in terms of virus detection. Our results demonstrate that xenosurveillance using blood-engorged tsetse flies is a valuable tool to track and survey viruses in wildlife in Sub-Saharan Africa.

ano.nymous@ccsd.cnrs.fr.invalid (Adeline Valente) 25 Sep 2023

https://hal.science/hal-04174029v1

[hal-04411441] Use of porcine intestinal organoids to study the transmissible gastroenteritis virus

To date, host-virus interactions have been studied mainly in cell cultures and/or animal models. These approaches come up against two problems: i) methodological, usually related to using immortalized cell lines, which can differ greatly from the target cells of the virus, and ii) ethical, related to experimenting with animals, which can induce varying degrees of symptoms and cause suffering and death. The recent development of organoids has made it possible to develop ex vivo models whose experimental conditions are significantly closer to physiological conditions. Using organoids makes it possible to plan to decrease animal experimentation greatly, in line with the 3Rs principle (Reduction, Refinement, Replacement), and each animal can potentially produce thousands of organoids from different tissues. The Viral Genetics and Biosafety Unit applies the porcine organoid system developed locally as part of the PigOrg project (of INRAE, ANSES and INSERM, funded by the Carnot Agrifood Transition Institute) to models of enteric coronavirosis in piglets, which has a strong impact on the pig industry. Here, we used the porcine transmissible gastroenteritis virus (TGEv) as a model, for which several strains of varying virulence exist and which can be cultivated on immortalized cells, to establish protocols of infections of different organoids (jejunum, duodenum, and ileum). Infections seem more effective for the jejunum than for the duodenum or ileum, and for viruses isolated on cells than on organ homogenate. This organoid system, which connects in vitro and in vivo conditions, will open novel and original perspectives into understanding the physiopathology of virus infections, especially deciphering hostpathogen interactions, without always needing to rely on extensive animal experiments.

ano.nymous@ccsd.cnrs.fr.invalid (Maud Contrant) 23 Jan 2024

https://hal.science/hal-04411441v1

[hal-04484150] Experimental study of infection with a new genotype of swine influenza virus that has spread in France and evaluation of vaccine protection

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Céline Deblanc) 29 Feb 2024

https://hal.science/hal-04484150v1

[hal-04303778] Characterization of particles exhaled by swine infected with an Influenza virus

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Lyes Ait Ali Yahia) 23 Nov 2023

https://u-pec.hal.science/hal-04303778v1

[hal-04225874] Vaccine safety of a new toxoid-based vaccine against Clostridioides difficile infection in rabbits

Clostridioides difficile infection (CDI) is a serious healthcare-associated disease, causing symptoms such as diarrhea. The main virulence factors responsible for the disease’s symptoms are two secreted cytotoxic proteins, toxin A (TcdA) and toxin B (TcdB). Treatment with antibiotics is difficult, as recurrent episodes of CDI usually occur in around 20-30% of patients after antibiotic therapy has ended. Several vaccines based on detoxified or recombinant forms of these toxins have been or are currently being tested in clinical trials. One of them is inactivated by formaldehyde, a method with obvious drawbacks. A new metal-catalyzed oxidation (MCO) method was used to detoxify the toxins while preserving the neutralizing epitopes. The aim of the project was therefore to combine these detoxified TxA and TxB toxins with a potent LiteVax adjuvant (LVA) to demonstrate vaccine safety and generate high levels of antibody responses in rabbits. For each study, 42 female rabbits, aged 8 weeks, were divided into 6 groups of 7 animals, each group vaccinated with different toxin concentrations (TxA between 5 and 20 µg and TxB between 20 and 80 µg) and different adjuvants (placebo, LVA adjuvant or alum). Each group was vaccinated three times at 14-day intervals by intramuscular route. Every day, the rabbits were observed for behavioral and feeding problems. Weekly kinetics were performed to determine serum and neutralizing antibody titers (against TcdA and TcdB), blood counts (cell populations) and inflammatory cytokines. White blood cell count and neutrophil percentage increased one day after immunization with LVA, but little or not with alum. Antibody titers were similar to those obtained with a conventional formaldehyde-inactivated CDI vaccine adjuvanted with alum. Alum enhanced antibody responses against TcdA but not against TcdB. LVA adjuvant generated significantly higher antibody responses against TcdB compared to alum. Histopathological analysis of the injection sites 42 days after the last injection showed no abnormal tissue reaction. In conclusion, MCO is an alternative method for the production of safe and immunogenic toxoid antigens, and TxA and TxB in combination with LVA adjuvant is a very interesting vaccine candidate against CDI.

ano.nymous@ccsd.cnrs.fr.invalid (Aria Aminzadeh) 03 Oct 2023

https://hal.inrae.fr/hal-04225874v1

[hal-04187670] The caecal microbiota promotes the acute inflammatory response and the loss of the intestinal barrier integrity during severe Eimeria tenella infection

Introduction Coccidiosis, a disease caused by intestinal apicomplexan parasites Eimeria , is a threat to poultry production. Eimeria tenella is one of the most pathogenic species, frequently causing a high prevalence of opportunistic infections. Objective The objective of this study is to investigate the role of the microbiota in the pathogenesis of severe Eimeria tenella infection. Methods We have previously shown that microbiota can promote parasite development. To study the effect of the microbiota on the pathogenesis of this infection, we used an experimental condition (inoculum of 10 000 oocysts E. tenella INRAE ) in which the parasite load is similar between germ-free and conventional broilers at 7 days post-infection (pi). Thirteen conventional and 24 germ-free chickens were infected. Among this latter group, 12 remained germ-free and 12 received a microbiota from conventional healthy chickens at 4 days pi. Caeca and spleens were collected at 7 days pi. Results Our results demonstrated caecal lesions and epithelium damage in conventional chickens at 7 days pi but not in germ-free infected chickens. Administration of conventional microbiota to germ-free chickens partially restored these deleterious effects. At day 7 pi, both infected conventional and germ-free chickens exhibited increased gene expression of inflammatory mediators, including IL15, IFNγ, TNFα and the anti-inflammatory mediator SOCS1 , whereas the inflammatory mediators CXCLi2, CCL20, IL18, CSF1, NOS2, PTGS2, IL1β, IL6 , the receptor CCR2 , and the anti-inflammatory mediators TGFβ1 and IL10 were upregulated only in infected conventional chickens. Notably, the IL18, PTGS2 gene expression was significantly higher in the infected conventional group. Overall, the inflammatory response enhanced by the microbiota might be in part responsible for higher lesion scores. Epithelial tight junction protein gene expression analysis revealed a significant upregulation of CLDN1 with the infection and microbiota, indicating a potential loss of the intestinal barrier integrity. Conclusion These observations imply that, during E. tenella infection, the caecal microbiota could trigger an acute inflammatory response, resulting in a loss of intestinal integrity. Increase in bacterial translocation can then lead to the likelihood of opportunistic infections. Hence, modulating the microbiota may offer a promising strategy for improving poultry gut health and limiting caecal coccidiosis.

ano.nymous@ccsd.cnrs.fr.invalid (Florian Tomal) 25 Aug 2023

https://hal.inrae.fr/hal-04187670v1

[hal-04143368] Physiopathology of Eimeria tenella infection and integrity of the intestinal barrier: influence of the microbiota

Eimeria tenella infection results in a severe intestinal disease leading to high economic impact in poultry industry. Coccidiosis is frequently associated with a high prevalence of opportunistic infections. Our objective was to study the importance of the microbiota on the physiopathology of the infection. Using an original model of germ-free and conventional broilers, our results show that, at a similar parasite load, lesions caused by E. tenella are dependent on the microbiota. At seven days post-infection, an increase of some inflammatory mediators is detected in the caecal tissue both in conventional and germ-free chickens whereas other inflammatory mediators are expressed only in a microbiota-dependent manner. Del Cacho et al 2014 showed that the neutralization of IL17A led to less lesions. In our study, IL-17A is increased only in conventional infected chickens. Administration of a conventional microbiota to germ-free chickens 4 days after infection restored caecal lesions and the expression of IL-17A. Among inflammatory cells producing IL-17A, we showed that T cells were the major producers suggesting that these cells may play a role in the physiopathology of this infection. Lesions represent a rupture of the intestinal barrier, which, at homeostasis, protects against invasion of commensal bacteria. Using a non-pathogenic E. coli strain administered by oral route, we confirmed a dissemination in the spleen during E. tenella infection. In conclusion, in E. tenella infection, the microbiota facilitates with a strong inflammatory response and the alteration of the intestinal barrier leading to bacterial translocation responsible for opportunistic infections.

ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Sadrin) 27 Jun 2023

https://hal.science/hal-04143368v1

[hal-03947262] Inflammatory Responses Induced by the Monophasic Variant of Salmonella Typhimurium in Pigs Play a Role in the High Shedder Phenotype and Fecal Microbiota Composition

Pigs infected with Salmonella may excrete large amounts of Salmonella, increasing the risk of spread of this pathogen in the food chain. Identifying Salmonella high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with Salmonella. Immune response was studied through total blood cell counts, production of anti-Salmonella antibodies and cytokines, and gene expression quantification. Total Salmonella shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences on the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with Salmonella induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to Salmonella modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing Salmonella high shedding in livestock. IMPORTANCE Salmonellosis remains the most frequent human foodborne zoonosis after campylobacteriosis and pork meat is considered one of the major sources of human foodborne infections. At the farm, host heterogeneity in pig infection is problematic. High Salmonella shedders contribute more significantly to the spread of this foodborne pathogen in the food chain. The identification of predictive biomarkers for high shedders could help to control Salmonella in pigs. The purpose of the present study was to investigate why some pigs become super shedders and others low shedders. We thus investigated the differences in the fecal microbial composition and the immune response in orally infected pigs presenting different Salmonella shedding patterns. Our data show that the proinflammatory response induced by S. Typhimurium at 1 dpi could be responsible for the modification of the fecal microbiota composition and functions observed mainly at 2 and 3 dpi and to the low and super shedder phenotypes.

ano.nymous@ccsd.cnrs.fr.invalid (Florent Kempf) 19 Apr 2023

https://hal.inrae.fr/hal-03947262v1

[hal-04416438] Microbiota promotes recruitment and pro-inflammatory response of caecal macrophages during E. tenella infection

Background: Eimeria genus belongs to the apicomplexan parasite phylum and is responsible for coccidiosis, an intestinal disease with a major economic impact on poultry production. Eimeria tenella is one of the most virulent species in chickens. In a previous study, we showed a negative impact of caecal microbiota on the physiopathology of this infection. However, the mechanism by which microbiota leads to the physiopathology remained undetermined. Macrophages play a key role in inflammatory processes and their interaction with the microbiota during E. tenella infection have never been investigated. We therefore examined the impact of microbiota on macrophages during E. tenella infection. Macrophages were monitored in caecal tissues by immunofluorescence staining with KUL01 antibody in non-infected and infected germ-free and conventional chickens. Caecal cells were isolated, stained, analyzed and sorted to examine their gene expression using high-throughput qPCR. Results: We demonstrated that microbiota was essential for caecal macrophage recruitment in E. tenella infection. Furthermore, microbiota promoted a pro-inflammatory transcriptomic profile of macrophages characterized by increased gene expression of NOS2, ACOD1, PTGS2, TNFα, IL1β, IL6, IL8L1, IL8L2 and CCL20 in infected chickens. Administration of caecal microbiota from conventional chickens to germ-free infected chickens partially restored macrophage recruitment and response. Conclusions: Taken together, these results suggest that the microbiota enhances the physiopathology of this infection through macrophage recruitment and activation. Consequently, strategies involving modulation of the gut microbiota may lead to attenuation of the macrophage-mediated inflammatory response, thereby limiting the negative clinical outcome of the disease.

ano.nymous@ccsd.cnrs.fr.invalid (Florian Tomal) 25 Jan 2024

https://hal.inrae.fr/hal-04416438v1

[hal-04171718] Développement d'un modèle murin de plaies pseudo-chroniques et soins péri-opératoires associés à la gestion de la douleur

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Christelle Rossignol) 26 Jul 2023

https://hal.inrae.fr/hal-04171718v1

[hal-04172380] Haemonchus contortus Adopt Isolate-Specific Life History Strategies to Optimize Fitness and Overcome Obstacles in Their Environment: Experimental Evidence

Gastrointestinal nematodes (GIN) use flexible life history strategies to maintain their fitness under environmental challenges. Costs incurred by a challenge to one life trait can be recouped by increasing the expression of subsequent life traits throughout their life cycle. Anticipating how parasites respond to the challenge of control interventions is critical for the long-term sustainability of the practice and to further ensure that the parasites withstand favourable adaptive responses. There is currently limited information on whether distinct populations of a GIN species respond to the same environmental challenge in a consistent manner, with similar alterations to their life history strategies or comparable fitness outcomes. This study compared the life history traits and experimental fitness of three distinct Haemonchus contortus isolates exposed to environmental challenges at both the parasitic (i.e., passage through resistant or susceptible sheep) and free-living (i.e., exposure to diverse climatic conditions) life stages. The key findings show that H. contortus maintain their fitness under challenge with isolate-specific alterations to their life history strategies. Further, partial exploration of the H. contortus isolates transcriptomes using cDNA-AFLP methods confirmed disparate expression profiles between them. These results bring fresh insights into our understanding of the non-genetic adaptive processes of GIN that may hinder the efficacy of parasite control strategies.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Chylinski) 27 Jul 2023

https://hal.inrae.fr/hal-04172380v1

[hal-04205854] In ovo administration of a phage cocktail partially prevents colibacillosis in chicks

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the main bacterial disease in poultry leading to significant economic losses worldwide. Antibiotic treatments favor the emergence of multidrug-resistant bacteria, and preventive measures are insufficient to control the disease. There is increasing interest in using the potential of bacteriophages, not only for phage therapy but also for prevention and biocontrol. This study aimed to evaluate the efficacy of a phage cocktail administered in ovo to prevent avian colibacillosis in chicks. When 4 different phages (REC, ESCO3, ESCO47, and ESCO58), stable under avian physiological conditions, were combined and inoculated at 17 embryogenic days (ED), they were transmitted to the newly hatched chicks. In a second trial, the 4-phage cocktail was inoculated into the allantoic fluid at ED16 and after hatch 1-day-old chicks were challenged with the O2 APEC strain BEN4358 inoculated subcutaneously. Two phages (REC and ESCO3) were still detected in the ceca of surviving chicks at the end of the experiment (7-days postinfection). Chicks that received the phages in ovo did not develop colibacillosis lesions and showed a significant decrease in intestinal BEN4358 load (8.00 × 107 CFU/g) compared to the challenged chicks (4.52 × 108 CFU/g). The majority of the reisolated bacteria from the ceca of surviving chicks had developed full resistance to ESCO3 phage, and only 3 were resistant to REC phage. The partially or complete resistance of REC phage induced a considerable cost to bacterial virulence. Here, we showed that phages inoculated in ovo can partially prevent colibacillosis in 1-wk-old chicks. The reduction in the APEC load in the gut and the decreased virulence of some resistant isolates could also contribute to control the disease.

ano.nymous@ccsd.cnrs.fr.invalid (Marianne Nicolas) 13 Sep 2023

https://hal.inrae.fr/hal-04205854v1

[hal-04171667] Établissement d'un modèle d'anse intestinale chez l'agneau nouveau-né afin d'évaluer de nouvelles méthodes de lutte contre les maladies entériques et de réduire l'utilisation d'animaux de laboratoire

Dans le but d'évaluer des alternatives naturelles pour contrôler la cryptosporidiose, infection entérique parasitaire affectant principalement les jeunes ruminants d'espèce de rente mais également l'être humain (zoonose), nous utilisons les agneaux comme espèce cible et comme modèle pour les animaux de plus grande taille comme les veaux. Nous avons pour objectif de stimuler les réponses immunitaires des animaux dès la naissance avec du colostrum supplémenté avec des produits naturels tels que des produits dérivés de levures qui contiennent des ligands des récepteurs de l'immunité innée. Cependant, la tolérance immunitaire intestinale s'installe rapidement après la naissance en réponse à la colonisation microbienne débutant dès la mise-bas par voie naturelle et par la suite via le colostrum, le lait et les multiples contacts avec l'environnement, et se caractérise par une hypo-réactivité aux antigènes microbiens (cf. modèles murins). Nous avons donc développé le modèle de chirurgie des anses intestinales sur agneaux nouveau-nés mis au monde par césarienne (et donc sans flore commensale) adapté à l'étude des interactions hôte-agent pathogène dans un environnement contrôlé et à l'évaluation de nouveaux composés antiparasitaires naturels in vivo. La possibilité de comparer différents produits naturels simultanément ainsi que des effets doses sur ce modèle, permet de réduire considérablement le nombre d’animaux expérimentaux à utiliser. Pour faciliter la réalisation de ces protocoles expérimentaux, nous utilisons notre troupeau d'ovins qui synchronise les mises-bas. Le jour de la chirurgie, la brebis est transférée dans la salle de chirurgie (confinement de niveau 2). Une césarienne est pratiquée et les agneaux sont réanimés. Après une courte phase de récupération, un agneau est choisi et transféré en salle de chirurgie. Il est installé sur une table de réanimation néonatale. Le protocole d'anesthésie / analgésie comprend : induction au masque (isoflurane), pose d'une sonde endotrachéale sous anesthésie locale (xylocaïne), maintien sous isoflurane (ventilation contrôlée), analgésie parentérale (buprénorphine), pose d'un cathéter veineux et mise sous perfusion, anesthésie locale traçante (lidocaïne). Pendant toute la procédure, les paramètres suivants sont surveillés : fréquences cardiaque et respiratoire, température rectale, SaO2, ETCO2. Une chirurgie à 4 mains est ensuite réalisée : - Extériorisation de la jonction iléo-caecale (IC) et de la portion distale de l'intestin grêle (IG)) ; - Ligatures avec création en général de triplicats - séparés par un inter-segment vide de "sécurité", y compris en amont et en aval de l'anse - (9 triplicats pour une anse de 50 cm environ) ; - Entérotomie en aval de l'anse ainsi créée, à proximité de la jonction IC, suture de l'intestin du côté de l'anse, puis idem en amont ; - Anastomose termino-terminale ; - Injection des préparations d'intérêt dans chaque segment. Pendant la chirurgie, une irrigation régulière de la portion externalisée de l'intestin est réalisée au sérum physiologique tiédi.

ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Kasal-Hoc) 26 Jul 2023

https://hal.inrae.fr/hal-04171667v1

[hal-04167063] Neutrophils expressing major histocompatibility complex class II molecules circulate in blood and milk during mastitis and show high microbicidal activity

Bovine mastitis is mainly caused by bacterial infection and is responsible for important economic losses as well as alterations of the health and welfare of animals. The increase in somatic cell count (SCC) in milk during mastitis is mainly due to the influx of neutrophils, which have a crucial role in the elimination of pathogens. For a long time, these first-line defenders have been viewed as microbe killers, with a limited role in the orchestration of the immune response. However, their role is more complex: we recently characterized a bovine neutrophil subset expressing major histocompatibility complex class II (MHC-II) molecules (MHC-II pos), usually distributed on antigen-presenting cells, as having regulatory capacities in cattle. In this study, our objective was to evaluate the implication of different neutrophils subsets in the mammary gland immunity during clinical and subclinical mastitis. Using flow cytometry, we analyzed the presence of MHC-II pos neutrophils in blood and in milk during clinical mastitis at different time points of inflammation (n = 10 infected quarters) and during subclinical mastitis, defined as the presence of bacteria and an SCC >150,000 cells/ mL (n = 27 infected quarters). Our results show, for the first time, that in blood and milk, neutrophils are a heterogeneous population and encompass at least 2 subsets distinguishable by their expression of MHC-II. In milk without mastitis, we observed higher production of reactive oxygen species and higher phagocytosis capacity of MHC-II pos neutrophils compared with their MHC-II neg counterparts, indicating the high bactericidal capacities of MHC-II pos neutrophils. MHC-II pos neutrophils are enriched in milk compared with blood during subclinical mastitis but not during clinical mastitis. Moreover, we observed a positive and highly significant correlation between MHC-II pos neutrophils and T lymphocytes present in milk during subclinical mastitis. Our experiments involved a total of 47 cows (40 Holstein and 7 Normande cows). To conclude, our study opens the way to the discovery of new biomarkers of mastitis inflammation.

ano.nymous@ccsd.cnrs.fr.invalid (Marion Rambault) 20 Jul 2023

https://hal.science/hal-04167063v1

[hal-04168152] Overexpression of Eimeria tenella Rhoptry Kinase 2 Induces Early Production of Schizonts

Eimeria tenella is an obligate intracellular parasite responsible for avian coccidiosis. Like other apicomplexan parasites, such as Toxoplasma gondii, cell invasion and intracellular development rely on apical organelle content discharge, named micronemes and rhoptries. Some rhoptry (ROP) kinases (ROPK) are key virulence factors in T. gondii. To date, among the 28 ropk genes carried by E. tenella, only two to four were confirmed by proteomic analysis or immunostaining to be expressed at the sporozoite stage. We have previously shown that EtROP1 is implicated in the inhibition of host cell apoptosis by interacting with the cellular p53. This work functionally described the second ROP kinase expressed at the sporozoite stage in E. tenella. EtROP2 is an active kinase that phosphorylates cell substrates of approximately 50 kDa. Its overexpression leads to the shortening of the prepatent period and to the early development of first-generation schizonts. Conduction of RNA sequencing analysis and reverse transcriptase quantitative PCR (RT-qPCR) on the host cell allowed us to identify the mitogen-activated protein kinase (MAPK) pathway and the transcription factor cFos to be upregulated by EtROP2. We also showed by immunofluorescence assay that the active kinase EtROP2 is implicated in the p38 MAPK pathway activation. We established here that EtROP2 activates the p38 MAPK pathway through a direct or indirect phosphorylation, leading to the overexpression of the master transcription factor cFos known to be implicated in E. tenella development. IMPORTANCE Rhoptries are specialized secretory organelles found in zoite stages of apicomplexan parasites. In addition to well-conserved rhoptry neck proteins, their protein consists mostly of kinase proteins, highly divergent from eukaryotic kinases. Some of those kinases are described as major virulence factors in Toxoplasma gondii, secreted into the host cell to hijack signaling pathways. Most of those kinases remain to be characterized in Eimeria tenella. Deciphering their cellular function is a prerequisite to supporting their relevance as a druggable target in development of new means of Eimeria tenella control. Secreted divergent kinases that interact with host cell partners to modulate pathways are good candidates, as they coevolve with their host targets to ensure their function within the host and are less prone to mutations that would lead to drug resistance. The absence of any orthologous kinase in host cells makes these parasite kinases a promising drug target candidate.

ano.nymous@ccsd.cnrs.fr.invalid (Adeline Ribeiro E Silva) 21 Jul 2023

https://hal.inrae.fr/hal-04168152v1

[hal-04167471] Isolation and Characterization of a Novel Phage Collection against Avian-Pathogenic Escherichia coli

The increase in antibiotic-resistant avian-pathogenic Escherichia coli (APEC), the causative agent of colibacillosis in poultry, warrants urgent research and the development of alternative therapies. This study describes the isolation and characterization of 19 genetically diverse, lytic coliphages, 8 of which were tested in combination for their efficacy in controlling in ovo APEC infections. Genome homology analysis revealed that the phages belong to nine different genera, one of them being a novel genus (Nouzillyvirus). One phage, REC, was derived from a recombination event between two Phapecoctavirus phages (ESCO5 and ESCO37) isolated in this study. Twenty-six of the 30 APEC strains tested were lysed by at least one phage. Phages exhibited varying infectious capacities, with narrow to broad host ranges. The broad host range of some phages could be partially explained by the presence of receptor-binding protein carrying a polysaccharidase domain. To demonstrate their therapeutic potential, a phage cocktail consisting of eight phages belonging to eight different genera was tested against BEN4358, an APEC O2 strain. In vitro, this phage cocktail fully inhibited the growth of BEN4358. In a chicken lethality embryo assay, the phage cocktail enabled 90% of phage-treated embryos to survive infection with BEN4358, compared with 0% of nontreated embryos, indicating that these novel phages are good candidates to successfully treat colibacillosis in poultry. IMPORTANCE Colibacillosis, the most common bacterial disease affecting poultry, is mainly treated by antibiotics. Due to the increased prevalence of multidrug-resistant avian-pathogenic Escherichia coli, there is an urgent need to assess the efficacy of alternatives to antibiotherapy, such as phage therapy. Here, we have isolated and characterized 19 coliphages that belong to nine phage genera. We showed that a combination of 8 of these phages was efficacious in vitro to control the growth of a clinical isolate of E. coli. Used in ovo, this phage combination allowed embryos to survive APEC infection. Thus, this phage combination represents a promising treatment for avian colibacillosis.

ano.nymous@ccsd.cnrs.fr.invalid (Marianne Nicolas) 20 Jul 2023

https://hal.inrae.fr/hal-04167471v1

[hal-04160330] The pUL51 Tegument Protein Is Essential for Marek’s Disease Virus Growth In Vitro and Bears a Function That Is Critical for Pathogenesis In Vivo

pUL51 is a minor tegument protein important for viral assembly and cell-to-cell spread (CCS) but dispensable for replication in cell culture of all Herpesviruses for which its role has been investigated. Here, we show that pUL51 is essential for the growth of Marek's disease virus, an oncogenic alphaherpesvirus of chickens that is strictly cell-associated in cell culture. MDV pUL51 localized to the Golgi apparatus of infected primary skin fibroblasts, as described for other Herpesviruses. However, the protein was also observed at the surface of lipid droplets in infected chicken keratinocytes, hinting at a possible role of this compartment for viral assembly in the unique cell type involved in MDV shedding in vivo. Deletion of the C-terminal half of pUL51 or fusion of GFP to either the N- or C-terminus were sufficient to disable the protein's essential function(s). However, a virus with a TAP domain fused at the C-terminus of pUL51 was capable of replication in cell culture, albeit with viral spread reduced by 35% and no localization to lipid droplets. In vivo, we observed that although the replication of this virus was moderately impacted, its pathogenesis was strongly impaired. This study describes for the first time the essential role of pUL51 in the biology of a herpesvirus, its association to lipid droplets in a relevant cell type, and its unsuspected role in the pathogenesis of a herpesvirus in its natural host. IMPORTANCE Viruses usually spread from cell to cell through two mechanisms: cell-released virus and/or cell-to-cell spread (CCS). The molecular determinants of CCS and their importance in the biology of viruses during infection of their natural host are unclear. Marek's disease virus (MDV) is a deadly and highly contagious herpesvirus of chickens that produces no cell-free particles in vitro, and therefore, spreads only through CCS in cell culture. Here, we show that viral protein pUL51, an important factor for CCS of Herpesviruses, is essential for MDV growth in vitro. We demonstrate that the fusion of a large tag at the C-terminus of the protein is sufficient to moderately impair viral replication in vivo and almost completely abolish pathogenesis while only slightly reducing viral growth in vitro. This study thus uncovers a role for pUL51 associated with virulence, linked to its C-terminal half, and possibly independent of its essential functions in CCS.

ano.nymous@ccsd.cnrs.fr.invalid (David Pasdeloup) 20 Jul 2023

https://hal.inrae.fr/hal-04160330v1

[hal-04226077] Evaluation des effets du traitement au plasma à froid sur le processus de cicatrisation des plaies pseudo-chroniques chez la souris : nouveau traitement alternatif aux antibiotiques

Les plaies chroniques constituent un problème de santé publique majeur, impactant à la fois les systèmes de soins et les patients victimes d’infections nosocomiales. Ces dernières années, l’apparition de résistances aux antibiotiques empêche une lutte efficace contre ces bactéries qui infectent ces plaies, empêchant par la même occasion une cicatrisation déjà altérée par certaines maladies (diabète). Afin de limiter l’utilisation répétée d’antibiotiques et de lutter contre les bactéries multirésistantes, une nouvelle technologie alternative a été créée : le traitement plasma froid. L’objectif est de mettre en évidence les effets du traitement plasma froid sur le processus de cicatrisation afin de tester ultérieurement comme d’éventuels traitements alternatifs pour lutter contre les bactéries résistantes aux antibiotiques. Les expérimentations ont été réalisées sur des souris C57Bl/6 et DBA/2 réparties en 3 lots de 18 souris par traitement (contrôle, plasma KinPen® (Argon) et plasma Multijet (Hélium/Oxygène). Selon un processus chirurgical préalablement défini, deux plaies dorsales de 4,5 mm ont été générées. Des attelles stériles en silicone ont été fixées autour des plaies et recouvertes d’un pansement pendant 5 jours. Des injections antalgiques et analgésiques ont été réalisées en phase post-opératoire pour limiter la douleur. Après retrait des attèles, les plaies ont été traitées pendant 1 minute durant 5 jours consécutifs par plasmas froids. Un suivi zootechnique et comportemental ont également été réalisés. Enfin, l’évolution des plaies a été scorée et la cicatrisation analysée par histologie. Une perte de poids a été constatée à J2 post-opératoire, avant un retour à la normale chez toutes les souris. Entre chaque traitement, une différence de lignée a été observé, montrant que la lignée C57bL/6 cicatrise plus vite que la lignée DBA/2, ce qui est amplifié par les traitements plasma à froid. Cependant, les deux traitements n’ont pas d’impact sur processus de cicatrisation, qui reste comparable à celui en absence de traitement. En conclusion, les deux lignées murines semblent présenter une constitution tissulaire différente influençant la cicatrisation de la peau. Il reste donc déterminer si ces traitements plasmas froids seront capables de désinfecter des plaies pseudochroniques infectées par S. aureus.

ano.nymous@ccsd.cnrs.fr.invalid (Christelle Rossignol) 03 Oct 2023

https://hal.inrae.fr/hal-04226077v1

[hal-04129892] The Brown Alga Bifurcaria bifurcata Presents an Anthelmintic Activity on All Developmental Stages of the Parasitic Nematode Heligmosomoides polygyrus bakeri

The current control of gastrointestinal (GI) parasitic nematodes mainly relies on the widespread use of anthelmintics, which has inevitably led to resistance. Therefore, there is an urgent need to find new sources of antiparasitic compounds. Macroalgae represent a rich source of active molecules and are widely described as having medicinal properties. In the present study, we investigated the potential anthelmintic activity of aqueous extracts from three species of algae (Bifurcaria bifurcata, Grateloupia turuturu and Osmundea pinnatifida) on the murine parasite Heligmosomoides polygyrus bakeri. Using a set of complementary in vitro tests, including larval development assays, egg hatching tests and nematicidal activity assays on larvae and adults, we report the nematicidal activity of aqueous extracts of B. bifurcata. In addition, aqueous extract fractionation using liquid/liquid partitioning with a solvent of increasing polarity was performed in order to identify the groups of active molecules underlying the anthelmintic activity. Non-polar extracts (heptane, ethyl acetate) demonstrated high anthelmintic potential, highlighting the role of non-polar metabolites such as terpenes. Here, we highlight the strong anthelmintic potential of the brown alga B. bifurcata on a mouse model of GI parasites, thus confirming the strong interest in algae as natural alternatives for the control of parasitic nematodes.

ano.nymous@ccsd.cnrs.fr.invalid (Morgane Miclon) 15 Jun 2023

https://hal.inrae.fr/hal-04129892v1

[hal-04175595] Evaluation of a Lateral Flow Immunochromatography Assay (LFIA) for Diagnosis and Surveillance of Brucellosis in French Alpine Ibex (Capra ibex)

France has been officially free of bovine brucellosis since 2005. Nevertheless, in 2012, as the source of two human cases, a bovine outbreak due to B. melitensis biovar 3 was confirmed in the French Alpine Bargy massif, due to a spillover from wild, protected Alpine ibex (Capra ibex). In order to reduce high Brucella prevalence in the local ibex population, successive management strategies have been implemented. Lateral flow immunochromatography assay (LFIA) was thus identified as a promising on-site screening test, allowing for a rapid diagnosis far from the laboratory. This study compared a commercial LFIA for brucellosis diagnosis with the WOAH-recommended tests for small ruminants (i.e., Rose Bengal test (RBT), Complement fixation test, (CFT) and Indirect ELISA, (iELISA)). LFIA showed the same analytical sensitivity as iELISA on successive dilutions of the International Standard anti-Brucella melitensis Serum (ISaBmS) and the EU Goat Brucella Standard Serum (EUGBSS). Selectivity was estimated at 100% when vaccinated ibex sera were analyzed. When used on samples from naturally infected ibex, LFIA showed high concordance, as well as relative sensitivity and specificity (&gt;97.25%) in comparison with RBT and CFT. This work shows high reliability and ensures a better standardization of LFIA testing for wild ruminants.

ano.nymous@ccsd.cnrs.fr.invalid (Luca Freddi) 02 Aug 2023

https://hal.inrae.fr/hal-04175595v1

[anses-04311996] Dissemination of IncI plasmid encoding bla CTX-M-1 is not hampered by its fitness cost in the pig’s gut

ABSTRACT Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase-producing Escherichia coli of animal origin. The extent of the burden imposed on the bacterial cell by these plasmids seems to modulate the emergence of “epidemic” plasmids. However, in vivo data in the natural environment of the strains are scarce. Here, we investigated the cost of a bla CTX-M-1 -IncI1 epidemic plasmid in a commensal E. coli animal strain, UB12-RC, before and after oral inoculation of 15 6- to 8-week- old specific-pathogen-free pigs. Growth rate in rich medium was determined on (i) UB12-RC and derivatives, with or without plasmid, in vivo and/or in vitro evolved, and (ii) strains that acquired the plasmid in the gut during the experiment. Although bla CTX-M-1 -IncI1 plasmid imposed no measurable burden on the recipient strain after conjugation and during the longitudinal carriage in the pig’s gut, we observed a significant difference in the bacterial growth rate between IncI1 plasmid-carrying and plasmid-free isolates collected during in vivo carriage. Only a few mutations on the chromosome of the UB12-RC derivatives were detected by whole-genome sequencing. RNA-Seq analysis of a selected set of these strains showed that transcriptional responses to the bla CTX-M-1 -IncI1 acquisition were limited, affecting metabolism, stress response, and motility functions. Our data suggest that the effect of IncI plasmid on host cells is limited, fitness cost being insufficient to act as a barrier to IncI plasmid spread among natural population of E. coli in the gut niche.

ano.nymous@ccsd.cnrs.fr.invalid (Margaux Allain) 28 Nov 2023

https://anses.hal.science/anses-04311996v1

[hal-04116035] Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

Background Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. Results We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. Conclusions We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.

ano.nymous@ccsd.cnrs.fr.invalid (Emilie Delpuech) 02 Jun 2023

https://hal.inrae.fr/hal-04116035v1

[hal-04322849] Un nouveau modèle d’étude des infections respiratoires à INRAE

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Alisson Niepceron) 05 Dec 2023

https://hal.inrae.fr/hal-04322849v1

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HAL : Dernières publications

[hal-04197473] Technological developments and 3D imaging for the diagnosis of aquaculture fish diseases

[hal-04197332] EcoXtract® green solvent increases rainbow trout performances and decreases susceptibility to VHSV

[hal-05095687] Plan de gestion des données de la plateforme d'infectiologie expérimentale des rongeurs et poissons

[hal-03955969] The influences of microbial colonisation and germ-free status on the chicken TCRβ repertoire

[hal-04175372] Differential Salmonella Typhimurium intracellular replication and host cell responses in caecal and ileal organoids derived from chicken

[hal-04417714] HTLV-1 biofilm polarization maintained by tetraspanin CD82 is required for efficient viral transmission

[hal-04230480] Tetraspanin CD82 maintains HTLV-1 biofilm polarization and is required for efficient viral transmission

[hal-04332121] A pig model of chronic hepatitis E displaying persistent viremia and a downregulation of innate immune responses in the liver

[hal-04320097] Caractérisation des particules exhalées par des porcs infectes par un virus influenza porcin

[anses-04123704] Evaluation of early single dose vaccination on swine influenza A virus transmission in piglets: From experimental data to mechanistic modelling

[hal-04057783] From In Vitro to In Vivo: A Rational Flowchart for the Selection and Characterization of Candidate Probiotic Strains in Intestinal Disorders

[hal-04175302] Recombinant viral hemorrhagic septicemia virus with rearranged genomes as vaccine vectors to protect against lethal betanodavirus infection

[hal-04177128] Staphylococcus epidermidis isolates from atopic or healthy skin have opposite effect on skin cells: potential implication of the AHR pathway modulation

[hal-04189068] Modulation of gut microbiota by antibiotics did not affect anhedonia in a high-fat diet-induced model of depression in male mice

[hal-04172440] Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

[hal-04344510] Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery

[hal-04271263] Non-Steroidal Estrogens Inhibit Influenza Virus by Interacting with Hemagglutinin and Preventing Viral Fusion

[hal-04229569] The Smallest Infectious Substructure Encoding the Prion Strain Structural Determinant Revealed by Spontaneous Dissociation of Misfolded Prion Protein Assemblies

[hal-04107725] Investigation of the Genus Flavobacterium as a Reservoir for Fish-Pathogenic Bacterial Species: the Case of Flavobacterium collinsii

[hal-04176764] Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to Cold Water Disease

[hal-04172998] Deficiency in hereditary hemorrhagic telangiectasia-associated Endoglin elicits hypoxia-driven heart failure in zebrafish

[hal-04116796] DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part II – the impact of lactation rank

[hal-04127637] DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part I – the impact of inflammation

[hal-04294675] Identification of a pharyngeal mucosal lymphoid organ in zebrafish and other teleosts: Tonsils in fish?

[hal-03943007] An Isolate of Streptococcus mitis Displayed In Vitro Antimicrobial Activity and Deleterious Effect in a Preclinical Model of Lung Infection

[anses-04228409] Controlled Experimental Infection in Pigs with a Strain of Yersinia enterocolitica Harboring Genetic Markers for Human Pathogenicity: Colonization and Stability

[anses-04040798] Research Note: Analysis of immune responses in broilers after vaccination against Campylobacter jejuni

[hal-04174029] Flying syringes for emerging enzootic virus screening: proof of concept for the devlopment of noninvasive xenosurveillance tools based on Tsetse flies

[hal-04411441] Use of porcine intestinal organoids to study the transmissible gastroenteritis virus

[hal-04484150] Experimental study of infection with a new genotype of swine influenza virus that has spread in France and evaluation of vaccine protection

[hal-04303778] Characterization of particles exhaled by swine infected with an Influenza virus

[hal-04225874] Vaccine safety of a new toxoid-based vaccine against Clostridioides difficile infection in rabbits

[hal-04187670] The caecal microbiota promotes the acute inflammatory response and the loss of the intestinal barrier integrity during severe Eimeria tenella infection

[hal-04143368] Physiopathology of Eimeria tenella infection and integrity of the intestinal barrier: influence of the microbiota

[hal-03947262] Inflammatory Responses Induced by the Monophasic Variant of Salmonella Typhimurium in Pigs Play a Role in the High Shedder Phenotype and Fecal Microbiota Composition

[hal-04416438] Microbiota promotes recruitment and pro-inflammatory response of caecal macrophages during E. tenella infection

[hal-04171718] Développement d'un modèle murin de plaies pseudo-chroniques et soins péri-opératoires associés à la gestion de la douleur

[hal-04172380] Haemonchus contortus Adopt Isolate-Specific Life History Strategies to Optimize Fitness and Overcome Obstacles in Their Environment: Experimental Evidence

[hal-04205854] In ovo administration of a phage cocktail partially prevents colibacillosis in chicks

[hal-04171667] Établissement d'un modèle d'anse intestinale chez l'agneau nouveau-né afin d'évaluer de nouvelles méthodes de lutte contre les maladies entériques et de réduire l'utilisation d'animaux de laboratoire

[hal-04167063] Neutrophils expressing major histocompatibility complex class II molecules circulate in blood and milk during mastitis and show high microbicidal activity

[hal-04168152] Overexpression of Eimeria tenella Rhoptry Kinase 2 Induces Early Production of Schizonts

[hal-04167471] Isolation and Characterization of a Novel Phage Collection against Avian-Pathogenic Escherichia coli

[hal-04160330] The pUL51 Tegument Protein Is Essential for Marek’s Disease Virus Growth In Vitro and Bears a Function That Is Critical for Pathogenesis In Vivo

[hal-04226077] Evaluation des effets du traitement au plasma à froid sur le processus de cicatrisation des plaies pseudo-chroniques chez la souris : nouveau traitement alternatif aux antibiotiques

[hal-04129892] The Brown Alga Bifurcaria bifurcata Presents an Anthelmintic Activity on All Developmental Stages of the Parasitic Nematode Heligmosomoides polygyrus bakeri

[hal-04175595] Evaluation of a Lateral Flow Immunochromatography Assay (LFIA) for Diagnosis and Surveillance of Brucellosis in French Alpine Ibex (Capra ibex)

[anses-04311996] Dissemination of IncI plasmid encoding bla CTX-M-1 is not hampered by its fitness cost in the pig’s gut

[hal-04116035] Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

[hal-04322849] Un nouveau modèle d’étude des infections respiratoires à INRAE