Clostridium perfringens is a major foodborne pathogen associated with meat products, yet its dissemination routes and persistence within slaughterhouses remain poorly understood. In this study, whole-genome sequencing combined with multilocus sequence typing (MLST), core genome MLST (cgMLST), and core single nucleotide polymorphism (SNP) analysis was applied to 286 C. perfringens isolates collected from cattle, pig, and poultry slaughterhouses in France. MLST analysis revealed extensive genetic diversity, with most isolates assigned to novel allelic profiles rather than previously described sequence types. Phylogenetic analyses based on cgMLST and SNP data revealed frequent recovery of closely related isolates from feces, meat, surfaces, and air, highlighting widespread dissemination of strains within slaughterhouses during processing. Notably, close genetic related isolates recovered from air and other sample types are consistent with air-associated dissemination within slaughterhouse environments. In addition, the detection of closely related strains across different sampling campaigns suggests the potential persistence of C. perfringens within slaughterhouse environments over time. Most isolates were classified as toxinotype A (97.9%), with a few belonging to toxinotypes D (1.0%) and G (1.0%), and in silico analyses revealed a broad distribution of virulence-associated genes. Antimicrobial resistance genes (ARGs) were commonly detected, particularly those conferring resistance to tetracyclines, although isolates carrying multiple ARGs remained infrequent. Overall, this study provides new insights into the genomic diversity, dissemination pathways, and persistence of C. perfringens in multi-species slaughterhouses. These findings highlight the potential role of air-associated dissemination in contamination dynamics and underscore the importance of improved hygiene control strategies to mitigate food safety risks along the meat production chain.
The Rapid evaporative ionization mass spectrometry (REIMS) technique enables real-time metabolite analysis of intact beef tissues, potentially predicting carcass traits and quality. Two 10-day aged muscles from 66 Limousine cows of a specific production system, rump (m. gluteus medius, RMP, n = 63) and striploin (m. longissimus thoracis, STR, n = 57) were measured using REIMS. The REIMS outputs were used to develop classification and prediction models via orthogonal partial to latent structures-discriminant (OPLS-DA). Variables studied included carcass traits (transport distance, muscle type, EUROP conformation, carcass weight, Meat Standards Australia (MSA) marbling score), laboratory measurements (intramuscular fat (IMF) content, Warner-Bratzler shear force (WBSF), compression force), and sensory traits (untrained consumer scores and the calculated meat-eating quality score (MQ4)). Variables were divided into two binary groups based on median values. The REIMS accurately distinguished RMP from STR muscles (test accuracy = 100%), and showed strong associations with transport distance, carcass traits, and laboratory measurements (R2Y = 0.86-0.94; Q2 = 0.55-0.78; test accuracy = 41.7%-66.7%). For sensory quality traits, RMP-based models achieved test accuracies of 63.3%-73.3%, while STR-based models failed to reliably predict any traits (test accuracies <60%). Tentative identification of REIMS features reflected the distinct intrinsic metabolic characteristics between the two muscles. Sensory quality traits in RMP were predominantly influenced by molecules involved in proteolysis and energy metabolism, whereas STR traits were primarily associated with lipid metabolism. These results highlight that REIMS is a rapid, muscle-specific evaluation tool, offering a promising alternative to traditional carcass grading and beef sensory quality assessment, especially in binary classification.
Livestock farming shapes the landscapes in the French Alps with stocking rates below 1 LU/ha and large areas of maintained pasture. The Decarbon'Alpes project studies the environmental performance of 41 herbivore farms, 49% of which use mountain pastures. Farms with the highest level of pastoralism generate the lowest climate impact per hectare. Compared to national standards, Alpine farms contribute more to biodiversity and better water quality but have a variable energy dependency. Greenhouse gas (GHG) emissions per unit of product are nevertheless higher due to lower animal productivity. The overall climate impact is significantly reduced when soil carbon sequestration is included through CAP'2ER (R). The measured carbon stocks in a selection of fields from the studied livestock alpine farms is 110 tC/ha at 0-30 cm, which exceed the French average on agriculture area. But annual stock variations accounted for by CAP'2ER (R) are only related to land use. Incorporating soil and climate as well as agricultural practices at different altitudes into C sequestration calculation by using CarSolEl on typical management fields case studies, indicates an average difference of -174 kg C/ha/year. Operationally, this more sensitive approach increases a lot the time required for the farm assessment, but it allows to simulate the effect on soil carbon of different adaptation strategy in response to climate change or to maintain soil fertility, which stimulates farmers-advisors exchange about smart climate farming. It seems easier to implement it in valleys and at mid-altitudes, due to better registration of agricultural practices and easier soil measurements to carry out to cover heterogeneity. These results highlight constraints to consider in perspective of future carbon farming certifications scheme, in line with ongoing European harmonization requirements.
In this study, the use of INOSYS data allows to position farms within the Jura Massif PDO system in relation to those in other mountain areas. PDO dairy farms in Franche-Comt & eacute; rely primarily on grass and legumes, with very limited use of external inputs, thus ensuring a high-quality, low-cost base ration. Between 2014 and 2023, these systems have maintained their grassland areas and protein selfsufficiency, while adapting herd size and stocking rates to climatic constraints. This consistency- combining grass-based feeding, low input use, and the production of high-quality milk-gives PDO farms remarkable economic and environmental resilience. Carbon balance analyses also reveal relatively low emission levels and significant carbon sequestration, resulting in a highly favorable net footprint.
Face à une demande croissante en produits laitiers caprins, l’utilisation de l’herbe permettrait de combiner réduction de la dépendance aux intrants alimentaires et transition agroécologique des élevages caprins. Trois systèmes, basés sur trois troupeaux de 55 chèvres se différenciant par leur période de mise-bas et leur stratégie de valorisation de prairies multi-espèces (PME) ont été conçus : un désaisonné bâtiment (DB), un désaisonné pâturant (DP) et un saisonné pâturant (SP). Les PME étaient valorisées au pâturage et/ou en foin séché en grange. Ni pesticides ni fertilisant azoté étaient apportés sur les 7 ha de PME et 3 ha de méteil du système DB ; et sur les 8 ha de PME et 2 ha de méteil des systèmes DP et SP. Les consommations et performances laitières de chaque troupeau ont été mesurées et les compositions botaniques, valeurs biochimiques et alimentaires des PME calculées de 2021 à 2023. Sur les trois ans et au sein des trois systèmes, les PDI variaient de de 50 à 52 g/kg MS pour les foins et de 47 à
