Labéo

We investigated the early-life interplay between microbiota, host, and environment by longitudinally monitoring nasal and gut microbiota in 30 veal calves over their first five months of life. Microbial composition and stability were highly compartmentalized. Fecal communities showed increasing biomass, diversity, and homogeneity with age. Conversely, nasal microbiota remained less diverse and highly variable between individuals, likely influenced by mucociliary clearance and transient colonization. Environmental factors, diet, and clinical indicators were associated with both microbial communities, alongside distinct cytokine profiles. As calves matured, microbiota dynamics and composition covaried across body sites, reflecting systemic immune development and environmental adaptations. This study provides a comprehensive, multi-layered characterization of microbial dynamics, identifying the first month of life as a critical window for interventions targeting the fecal microbiota. The nasal microbiota, by contrast, remains flexible and amenable to modulation throughout the production cycle.Supplementary InformationThe online version contains supplementary material available at 10.1186/s42523-025-00494-w.

Since 2014, mass mortalities of mussels Mytilus spp. have occurred in production areas on the Atlantic coast of France. The aetiology of these outbreaks remained unknown until the bacterium Francisella halioticida was detected in some mussel mortality cases. This retrospective study was conducted to assess the association between F. halioticida and these mussel mortalities. Mussel batches (n = 45) from the Atlantic coast and English Channel were selected from archived individual samples (n = 863) collected either during or outside of mortality events between 2014 and 2017. All mussels were analysed by real-time PCR assays targeting F. halioticida; in addition, 185 were analysed using histological analysis and 178 by 16S rRNA metabarcoding. F. halioticida DNA was detected by real-time PCR and 16S rRNA metabarcoding in 282 and 34 mussels, respectively. Among these individuals, 82% (real-time PCR analysis) and 76% (16S rRNA metabarcoding analysis) were sampled during a mortality event. Histological analyses showed that moribund individuals had lesions mainly characterized by necrosis, haemocyte infiltration and granulomas. Risk factor analysis showed that mussel batches with more than 20% of PCR-positive individuals were more likely to have been sampled during a mortality event, and positive 16S rRNA metabarcoding batches increased the strength of the association with mortality by 11.6 times. The role of F. halioticida in mussel mortalities was determined by reviewing the available evidence. To this end, a causation criteria grid, tailored to marine diseases and molecular pathogen detection tools, allowed more evidence to be gathered on the causal role of this bacterium in mussel mortalities.

Equine influenza virus (EIV) remains a threat to horses, despite the availability of vaccines. Strategies to monitor the virus and prevent potential vaccine failure revolve around serological assays, RT-qPCR amplification, and sequencing the viral hemagglutinin (HA) and neuraminidase (NA) genes. These approaches overlook the contribution of other viral proteins in driving virulence. This study assesses the potential of long-read nanopore sequencing for fast and precise sequencing of circulating equine influenza viruses. Therefore, two French Florida Clade 1 strains, including the one circulating in winter 2018–2019 exhibiting more pronounced pathogenicity than usual, as well as the two currently OIE-recommended vaccine strains, were sequenced. Our results demonstrated the reliability of this sequencing method in generating accurate sequences. Sequence analysis of HA revealed a subtle antigenic drift in the French EIV strains, with specific substitutions, such as T163I in A/equine/Paris/1/2018 and the N188T mutation in post-2015 strains; both substitutions were in antigenic site B. Antigenic site E exhibited modifications in post-2018 strains, with the N63D substitution. Segment 2 sequencing also revealed that the A/equine/Paris/1/2018 strain encodes a longer variant of the PB1-F2 protein when compared to other Florida clade 1 strains (90 amino acids long versus 81 amino acids long). Further biological and biochemistry assays demonstrated that this PB1-F2 variant has enhanced abilities to abolish the mitochondrial membrane potential ΔΨm and permeabilize synthetic membranes. Altogether, our results highlight the interest in rapidly characterizing the complete genome of circulating strains with next-generation sequencing technologies to adapt vaccines and identify specific virulence markers of EIV.

Equine influenza virus (EIV) is responsible for recurring outbreaks that are detrimental to the equine industry. Vaccination is key for prevention, but the effectiveness and duration of protection provided by existing vaccines is often insufficient. In order to improve vaccine efficacy, we evaluated the benefit of immune stimulation with inactivated Parapoxvirus ovis (iPPVO) on the antibody response induced by a vaccine boost against EIV. A whole inactivated ISCOMatrix-adjuvanted equine influenza vaccine was administered alone (n = 10) or combined with iPPVO injections at D0, D2 and D4 post vaccination (n = 10) to adult horses that required a vaccine boost 6 months after the last immunization, as now recommended by the WOAH. Antibody levels were measured with the single radial haemolysis (SRH) assay at 1, 3 and 6 months post-vaccination. Results revealed that horses that received iPPVO had higher antibody levels than the control group injected with the EI vaccine alone. Although the vaccine used contains only a clade 1 and European lineage strain, the increase in protective antibodies was also observed against a clade 2 strain. Thus, immune stimulation with iPPVO, a substance already marketed as an immunostimulant, could be used to improve vaccination protocols in horses and potentially other species.

International audience

Background: Equine herpesvirus type-1 (EHV-1) is an important threat to the equine industry, as illustrated by the ongoing outbreak of neurological disease that was initially reported during a large equestrian event in Valencia, Spain in 2021. Horses returning from this event to their training yards have contributed to the spread of the virus to nine other European countries and to Qatar. Objectives: To design a “tracking” marker in order to specifically follow the dissemination of the Valencia strain, in EHV-1 infected horses with no known epidemiological link with the Valencia outbreak. Study design: Strain isolation and genome sequences’ comparison. Methods: 67 nasopharyngeal swab samples from horses stationed in Valencia were analysed by EHV-1 qPCR and a rapid A/G/C2254 (ORF30) typing test. Positive samples were used for strain isolation in vitro, and Multilocus Sequence Typing (MLST). Results: 19/67 (28%) samples were EHV-1 positive (all 19 typed as A2254). Two strains (FR/Valencia1/2021 and FR/Valencia2/2021) were successfully isolated and characterised by MLST as belonging to clade 10. Analysis of the MLST ORF sequences revealed a mutation at position 713 of the ORF11 (A713G) in FR/Valencia1/2021 and FR/Valencia2/2021, when compared with reference strains Ab4 and V592. This A713G mutation was not present in 104 ORF11 sequences obtained from Genbank (strains from the UK, USA, China, Australia, Belgium, New-Zealand, Japan or India), or 131 and 14 ORF11 sequences from strains isolated in Ireland or France, respectively. This marker allowed subsequent confirmation of suspicious epidemiological links in EHV-1 cases. Main limitation: The limited number of ORF11 sequences available in some countries. Conclusions: Although the existence of this mutation in other field strains cannot be excluded, its absence in the 249 ORF11 sequences analysed, suggests that this SNP constitutes an interesting epidemiological marker to identify horses infected with the EHV-1 strain which was associated with the outbreak in Valencia.

International audience

A herd of seven captive-born Grevy's zebras (Equus grevyi) experienced an outbreak of nasal discharge and sneezing. Clinical signs, including lethargy and anorexia, were severe and acute in three animals, including a 16-mo-old male that died within 48 h. Treatment of two severely affected zebras included valacyclovir (40 mg/kg PO), meloxicam (0.6 mg/kg IM/PO), and cefquinome (2.5 mg/kg IM q48h). An adult female improved rapidly, and clinical signs resolved within 48 h of treatment. Administration of valacyclovir pellets was very complicated in a 2-mo-old female, and death occurred within 48 h. Histologic examination of the two individuals that died revealed severe fibrinonecrotic interstitial pneumonia with prominent hyaline membranes and type II pneumocyte hyperplasia. Additionally, the 16-mo-old male presented systemic endothelial activation with vascular thrombosis and necrosis and mild nonsuppurative meningoencephalitis. Herpesviral DNA was detected in the lungs of both individuals by nested polymerase chain reaction. The nucleic acid sequence of the amplicons showed 100% similarity with previously published equid alphaherpesvirus 9 sequences. Three additional animals developed mild nasal discharge only and recovered spontaneously. The zebras shared housing facilities with other species, including white rhinoceros (Ceratotherium simum), reticulated giraffe (Giraffa camelopardalis reticulata), and several antelope species. None of these animals showed clinical signs. Additionally, nasal swabs and whole blood samples were collected from cohoused white rhinoceroses (n = 3) and springboks (Antidorcas marsupialis, n = 3) as well as nasal swabs from cohoused reticulated giraffes (n = 4). Nucleic acid sequence from equid herpesviruses was not detected in any of these samples. The source of the infection in the zebras remains unclear.