HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Optimizing contact tracing for avian influenza in poultry flocks
No full textInternational audienceContact tracing is commonly used to manage infectious diseases of both humans and animals. It aims to detect early and control potentially infected individuals or farms that had contact with infectious cases. Because it is very resource-intensive, contact tracing is usually performed on a pre-defined time window, based on previous knowledge of the duration of the incubation period. However, pre-defined time windows may not be always relevant, reducing the efficiency of contact tracing. In this study, we estimated the day when farms were first infected with highly pathogenic avian influenza viruses, a devastating pathogen causing severe socio-economic damage in domestic poultry. The estimation was performed by fitting a stochastic mechanistic model to observed daily mortality data from 63 infected poultry farms in France and The Netherlands, using approximate Bayesian computation. Independent of the poultry species or country, the estimates of the time of first infection ranged between 3.4 (95% credible interval—CrI: 2.6, 4.6) and 19.9 (95% CrI: 11.9, 31.3) days prior to the last observation. We developed an online application to provide real-time support to policymakers by estimating realistic ranges of dates of first infection to inform contact tracing and improve its efficiency
Equine piroplasmosis in different geographical areas in France: prevalence heterogeneity of asymptomatic carriers and low genetic diversity of Theileria equi and Babesia caballi
No full textInternational audienceEquine piroplasmosis is a worldwide tick-borne disease caused by the protozoan parasites Theileria equi and Babesia caballi , with significant economic and sanitary consequences. It can also limit the export of infected horses to piroplasmosis-free countries. These two parasites are genetically variable, with greater diversity observed in T. equi . This variability can potentially impact diagnostic accuracy. Our study aimed to evaluate the frequency of asymptomatic carriers of these parasites in France and describe the circulating genotypes. We used a species-specific nested PCR protocol targeting the 18S small subunit (SSU) rRNA gene and subsequent amplicon sequencing on blood samples collected from 566 asymptomatic horses across four National Veterinary Schools. The carrier frequency varied considerably, ranging from 18.7% around Paris (central-north) to 56.1% around Lyon (southeast), with an overall prevalence of 38.3%. T. equi carriers were ten times more frequent (91.7%, 209/228 isolates) compared to B. caballi carriers (8.8%, 19/228 isolates). Notably, T. equi carrier frequency was significantly lower in the northern region (Ile de France) compared to the southeastern regions. Interestingly, a strong correlation was observed between the frequencies of asymptomatic carriers and reported cases of acute piroplasmosis across all four geographic areas. Neither gender (female, gelding, or stallion) nor horse age showed a significant effect on the frequency of asymptomatic carriers. In areas with the highest carrier frequency, a substantial proportion of horses (22.2% to 37.5%) carried T. equi before the age of three, indicating high infection pressure. Genotyping of 201 T. equi isolates revealed a predominance of genotype E (98%), with only a few isolates belonging to genotype A (2%). Notably, two of the four genotype A isolates were detected in horses originating from Spain. All 19 B. caballi isolates belonged to the most common genotype A of this species. The discussion section explores the link between these results, the tick distribution and abundance, and the frequency of detection of T. equi and B. caballi in febrile cases attributed to piroplasmosis
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization
No full textInternational audienceThe recent rapid radiation of Tillandsia subgenus Tillandsia (Bromeliaceae) provides an attractive system to study the drivers and constraints of species diversification. This species-rich Neotropical monocot clade includes predominantly epiphytic species displaying vast phenotypic diversity. Recent in-depth phylogenomic work revealed that the subgenus originated within the last 7 myr, with one major expansion from South into Central America within the last 5 myr. However, disagreements between phylogenies and lack of resolution at shallow nodes suggest that hybridization may have occurred throughout the radiation, together with frequent incomplete lineage sorting and rapid gene family evolution. We used whole-genome resequencing data to explore the evolutionary history of representative ingroup species employing both tree-based and network approaches. Our results indicate that lineage co-occurrence does not predict relatedness and confirm significant deviations from a tree-like structure, coupled with pervasive gene-tree discordance. Focusing on hybridization, ABBA-BABA and related statistics were used to infer the rates and relative timing of introgression, whereas topology weighting uncovered high heterogeneity of the phylogenetic signal along the genome. High rates of hybridization within and among subclades suggest that, contrary to previous hypotheses, the expansion of subgenus Tillandsia into Central America proceeded through several dispersal events, punctuated by episodes of diversification and gene flow. Network analysis revealed reticulation as a plausible propeller during radiation and establishment across different ecological niches. This work contributes a plant example of prevalent hybridization during rapid species diversification, supporting the hypothesis that interspecific gene flow facilitates explosive diversification
An optimized protocol to detect high‐throughput DNA methylation from custom targeted sequences on 96 samples simultaneously
No full textInternational audienceGenome methylation represents an important source of regulation of gene expression. To date, custom molecular tools for studying targeted regions of the genome are restricted to several megabases. We developed a protocol to epigenotype differentially methylated CpGs in specific regions of the genome. The protocol describes a targeted methylation library preparation upstream short read sequencing with an Illumina instrument. The protocol includes the New England Biolabs Next Enzymatic Methyl‐seq Library Preparation workflow combined with the Twist Bioscience Targeted Methylation Sequencing workflow. The protocol is divided into eight steps: fragmentation, library preparation, enzymatic conversion, indexing, pooling, hybridization, capture, and amplification. Main advantages are (a) a lower amount of DNA (100 and 50 ng) than other technologies, (b) the limitation of DNA degradation using enzymatic conversion instead of chemical bisulfite, (c) the pooling of samples into 8‐plex reducing handling time, and (d) the significant reduction of the panel quantity divided by 20 for saving experimental costs. This protocol was carried out on 96 samples simultaneously in a standard molecular biology laboratory, and the multiplexing can be run up to 384 samples for methylation experiments. We developed a high‐throughput epigenotyping method as an alternative of methylation arrays. This approach can be adapted to any interesting regions using a custom panel for agronomic species and model organisms
Printable biomaterials for 3D brain regenerative scaffolds: An in vivo biocompatibility assessment
No full textInternational audienceBackgroundBrain regeneration after injury is a challenge being tackled by numerous therapeutic strategies in pre-clinical development. There is growing interest in scaffolds implanted in brain lesions. Developments in 3D printing offer the possibility of designing complex structures of varying compositions adapted to tissue anatomy.MethodsThis feasibility study assessed the cerebral biocompatibility of four bioeliminable Digital Light Processing (DLP) printed materials in the rat model: gelatin methacrylate (GelMA), poly(ethylene glycol)diacrylate (PEGDA) mixed with GelMA (PEGDA-GelMA), poly(trimethylene carbonate) trimethacrylate (PTMC-tMA) and an ABA triblock copolymer of polypropylene fumarate-b-poly γ-methyl ε-caprolactone-b-polypropylene fumarate (P(PF-MCL-PF)). Their tolerance was compared to that of polydioxanone Ethicon (PDSII), a neurosurgery suture component commonly used in clinical practice. A one-month MRI and behavioral follow-up aided in safety assessment.ResultsHigh-resolution T2 MRI imaging effectively captured the scaffold structures and demonstrated its non-invasive utility in monitoring degradability. PDSII served as a control of the acceptable inflammatory response to implantable foreign bodies. GelMA, PEGDA-GelMA and PTMC-tMA did not affect the permissive glial barrier, promoted cell migration, and neovascularization without additional perilesional microglial inflammation (median mean of 6.5 %, compared to 8.2 % for the PDSII control). However, the GelMA scaffold core was not colonized and allowed a limited neuronal progenitors recruitment. The rigidity of PTMC-tMA facilitated insertion, but posed histological issues. The brain hardly reacted to the P(PF-MCL-PF).ConclusionAll these materials can serve as a basis for brain regeneration. PEGDA-GelMA emerged as a promising candidate for intracerebral implantation, combining biophysical and bioprinting advantages while maintaining an acceptable level of inflammation compared with clinically used suture, paving the way for innovative therapies
Using the transmissibility model to demonstrate transgenerational transmission of environmental effects in quails
No full textInternational audienceNon-genetic information, such as epigenetic modifications, can modulate gene expression and influence phenotypic outcomes. Additionally, these modifications can be transmitted across generations, contributing to transgenerational phenotypic variation independent of changes in the DNA sequence. The present study aimed to demonstrate the vertical transmission of environmental effects. We used an experimental design in quails with two epilines: a control line and a treatment line (Epi-/Epi+). Females in the Epi+ line were fed a genistein-supplemented diet. Reproduction of these lines was then conducted in a mirrored mating design over three generations, with a total of 1,566 animals phenotyped. We used the transmissibility model with environment with fixed effects of rearing condition, sex, generation, age at the time of measurement and direct effect of the genistein (on the animal, embryo and germ cells). We added to the model the random effect of the transmissible potential of the animal, which transmissibility matrix contains sire and dam path coefficients of transmission. These coefficients have to be estimated conversely to the genetic model where they are fixed to 0.5, and, moreover an additional covariance (r) for offspring of genistein-fed dams which is then transmitted to next generations via sires and dams. In the transmissibility model with environment, the proportion of transmitted variance of body weights varied from 0.36 (at 1 week) to 0.73 (at 7 weeks). The covariance (r) was significantly different from zero for body weight traits, indicating a transgenerational transmission of genistein's effects. This value corresponded to a high correlation at one week (0.44) but low for other body weight traits (lower than 0.02).The findings demonstrated the transgenerational transmission of environmental effects induced by genistein on body weight traits in quails, indicating that environmental factors can potentially influence multiple generations. Using these results may enhance the effectiveness of genetic selection by accelerating the response to selection for traits of interest, which is crucial for accelerating adaptation to environmental challenges
Valorization of feral pigs in the tropics, from the genetic characterization to the re-domestication
No full textInternational audienceFeral pigs may serve as a valuable genetic resource for the future, offering potential interesting gene pool for adaptation to climate change and the preservation of biodiversity. The main objective of this study was to identify the genetic structure of feral pigs from the Caribbean island of Martinique, measure the inbreeding rate of a Creole population re-domesticated in 2016 from captured feral pigs, and evaluate its evolution to the present day. We hypothesized that feral pigs, like Creole breeds of the Americas, have been shaped by a unique cross-breeding process linked to the historical context of the Caribbean. A total of 121 animals were genotyped and 76 were compared with referenced mainstream genotypes and Creole breeds from the Americas. Re-domestication efforts were carried out through a holistic approach, involving researchers, farmers, consultants, and development actors. The results showed that feral and semi-feral pigs in Martinique belong to the creole pig breeds, with more than 20% Iberian genetic admixture. The majority of domesticated pigs groups studied including re-domesticated creole pigs exhibit a significantly lower proportion of runs of homozygosity compared to feral pigs, suggesting a better control of inbreeding, thanks to structured breeding programs. The chosen conservation strategy was the result of a consensus between scientific evidence, practical experience, and field feasibility. A rotational mating system using sire lines among a minimum of five farmers was adopted. This approach is expected to generate, within five years, a pedigree containing information on a total of at least 150 reproducers on 8 generations
Transcriptomic analysis of the interactions between Fibrobacter succinogenes S85, Selenomonas ruminantium PC18 and a live yeast strain used as a ruminant feed additive
No full textInternational audienceMicrobes inhabiting the rumen convert fibrous plant material into usable energy for the host ruminant through a sophisticated network of microbial interactions. Metabolite crossfeeding is considered a key feature of the rumen microbiome, enhancing its stability, productivity, and efficiency in degrading plant material. This study analysed in vitro the metabolic interactions between two key rumen bacteria: the cellulolytic bacterium Fibrobacter succinogenes S85 and the saccharolytic bacterium Selenomonas ruminantium PC18. Additionally, the impact of Saccharomyces cerevisiae CNCM I-1077 on their metabolism and interactions was investigated. This strain is used as a feed additive for ruminants.ResultsBacteria were cultured on either cellobiose or cellulose as carbon substrates. Interactions were studied through RNA-seq transcriptomic analysis of various microbial combinations, alongside substrate consumption and metabolite production measurements. The results revealed crossfeeding between F. succinogenes and S. ruminantium, as well as a significant upregulation of numerous F. succinogenes CAZyme genes in response to cellulose. The presence of the yeast strain under the different culture conditions induced metabolic and gene expression changes in both F. succinogenes and S. ruminantium. Notably, no lactate was detected when the yeast was added to S. ruminantium cultures or cocultures. Furthermore, the presence of bacteria influences yeast metabolism and crossfeeding between bacteria and yeast was suggested.ConclusionsThe findings provide deeper insight into the in vitro interactions between F. succinogenes, S. ruminantium and S. cerevisiae, highlighting possible modes of action that may explain some of the observed positive effects of yeast on rumen function in vivo. This study underscores the mutual interactions between rumen bacteria and live yeast
Small intestinal bacterial overgrowth in children: An expert review by the ESPGHAN Gastroenterology Committee
No full textInternational audienceThe aim of this review is to summarize the prevalence, etiology, pathogenesis, diagnosis, and treatments currently available for small intestinal bacterial overgrowth (SIBO) in children. SIBO is a clinical entity characterized by the presence of an excessive number of bacteria in the small bowel leading to several nonspecific gastrointestinal symptoms due to malabsorption and malnutrition, such as bloating, flatulence, belching, diarrhea, abdominal pain, nausea, steatorrhea, fatigue and stunted growth. Initially thought to develop specifically in the context of abnormal or postsurgical gastrointestinal anatomy, it has then been recognized that it can be associated with other nonsurgical conditions, such as gastrointestinal dysmotility, disorders of gut–brain interactions and chronic use of drugs. The uncertainty regarding the exact cut‐off of excessive number of bacteria in the small bowel has led to the absence of a universally accepted definition of SIBO making well‐designed research to assess the best diagnostic and therapeutic approaches challenging. Current available diagnostic tools includes duodenal/jejunal aspirate with culture and hydrogen breath tests, which all have some limitations and pitfalls that prevent accurate sampling. The treatment goal should be to treat the underlying causes, restore the healthy intestinal microflora, relieve the symptoms and address the associated complications. The use of antibiotics represents the treatment cornerstore. However, they are commonly used despite the scarce published evidence and the absence of agreement on the dose and duration of the treatment. Currently, data on best diagnostic and therapeutic strategies in children remain lacking. Novel diagnostic approaches for SIBO are emerging and may facilitate further research
Characterization of prion strains and peripheral prion infectivity patterns in E200K genetic CJD patients
No full textInternational audienceThe mutation E200K in the prion protein gene (PRNP) is the most common variant in genetic Creutzfeldt-Jakob disease (gCJD). The clinical and pathological features observed in patients with E200K gCJD led to the hypothesis that the prion strains responsible for this form of the disease may be related to those involved in sporadic CJD (sCJD). In this study, we characterized the prion strains responsible for E200K gCJD cases from Slovakia (n = 12), Spain (n = 9), and France (n = 3) using transgenic mouse models expressing human prion protein (PrP). The cohort included patients with various PRNP genotypes: E200K-Met 129 /Met 129 , E200K-Met 129 /E200K-Met 129 , E200K-Met 129 /Val 129 , and E200K-Val 129 /Val 129 . Prion strain characterization revealed that the strains isolated from E200K gCJD cases corresponded to the two most common strains identified in sCJD cases: M1 CJD and V2 CJD . Depending on the individual, these strains were either present as pure M1 CJD or V2 CJD , or as a mixture of both (M1 CJD + V2 CJD ). Additionally, peripheral tissues from E200K-Met 129 /Met 129 patients (n = 4) and one E200K-Met 129 /Val 129 case were analyzed for prion infectivity and seeding activity. Similar to sCJD patients, low but detectable levels of prions were found in various peripheral tissues of E200K gCJD cases. Overall, our findings suggest that the prion strains and their distribution in the body are highly similar between E200K gCJD and sCJD patients. These similarities indicate that individuals carrying the E200K mutation may serve as a valuable model for understanding CJD pathogenesis during the preclinical phase of the disease