Molecular and eco-epidemiology of Leptospira borgpetersenii serovar Ballum in wild invasive mammals in a farming environment in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand

Leptospirosis is an important zoonosis in New Zealand where it has historically been associated with livestock. Formerly negligible in human cases notified, Leptospira borgpetersenii serovar Ballum—associated with rodents and hedgehogs (Erinaceus europaeus)—is now preponderant. The role of wild introduced mammals in the epidemiology of leptospirosis has been overlooked in New Zealand but remains a critical question. In this thesis, we determined the prevalence of Leptospira serovars, renal colonisation and seroprevalence in wild mammals and sympatric livestock. During a cross-sectional and a longitudinal survey, house mice (Mus musculus), ship rats (Rattus rattus) and hedgehogs were trapped in farms with a history of leptospirosis to collect sera and kidneys. Urine and sera from livestock (dairy or beef cattle, sheep) and dogs were also collected on the same farms. Sera were tested by microagglutination test to identify serovars/serogroups that circulate in wildlife for comparison with those circulating in livestock. Urine and kidney samples were used to determine prevalence by qPCR, to isolate circulating leptospires by culture and subject them to whole genome sequencing, in order to determine their phylogenetic relationships and compare them to other sequences locally, nationally and internationally. Capture-mark recapture (CMR) methods were used to investigate the population dynamics of mice naturally infected with Ballum. Finally, the level of lesions and bacterial load in kidneys were assessed visually by histopathology and put in perspective with other results to investigate reservoir dynamics. Direct or indirect presence of Ballum was found in all wild and domestic species investigated. Overall apparent prevalence in mice, rats and hedgehogs was respectively 46%, 95% CI [39, 52%], 44% [26, 62%] and 27% [11, 50%]. It varied greatly between seasons in mice, with a spring peak (83 to 86%) and minimum in autumn (31 to 37%). Mice densities reached up to 56 mice/ha and varied seasonally in the opposite way, resulting in a relatively constant density of infected mice, ranging 3-8 infected mice/ha. An extremely low rate of mutations hindered the investigation of transmission pathways using genomics. However, despite little or no lesions in all species, the bacterial load was markedly higher in mice, suggesting rats and hedgehogs are secondary hosts. Control strategies to mitigate exposure to Leptospira in NZ should include wild mammals, and especially mice

Etude comparative de la Leptospirose chez le Vison d'Europe (Mustela lutreola) et les autres petits carnivores du Sud-Ouest de la France

Le Vison d'Europe (Mustela lutreola) est une espèce semi-aquatique très menacée. La prévalence et l'importance de la leptospirose chez les petits carnivores sauvages ainsi que le rôle épidémiologique de ces derniers sont méconnus. Pour évaluer le rôle de la maladie dans le déclin du Vison d'Europe, nous avons estimé la séroprévalence et le taux de portage rénal de leptospires pathogènes chez 6 espèces de petits carnivores sympatriques en utilisant les techniques de microagglutination et de PCR. La séroprévalence s'est révélée très élevée, surtout chez les Mustélidés vivant en milieu humide et en contact avec des rongeurs. Ils peuvent excréter des leptospires mais leur rôle comme réservoir doit être confirmé. Aucun symptôme aigu n'a été observé, mais la fragilité des populations de Vison d'Europe associée à des lésions chroniques qui restent à démontrer pourrait avoir des conséquences démographiques.NANTES-BU Médecine pharmacie (441092101) / SudocTOULOUSE-EN Vétérinaire (315552301) / SudocNANTES-Ecole Nat.Vétérinaire (441092302) / SudocSudocFranceF

L'essor des dispositifs communicationnels stratégiques dans le système des inforoutes et de la communication internationale. Dérive des contenus versus stratégie des dispositifs

Fayard Pierre-Marie, Moinet Nicolas. L'essor des dispositifs communicationnels stratégiques dans le système des inforoutes et de la communication internationale. Dérive des contenus versus stratégie des dispositifs. In: Communication. Information Médias Théories, volume 17 n°1, printemps 1996. pp. 227-235

Spatio-temporal dynamics of tularemia in French wildlife: 2002–2013

International audienceTularemia, caused by Francisella tularensis, is endemic in France. The surveillance of this disease in wildlife is operated by the SAGIR Network and by the National Reference Laboratory for Tularemia. Wild animals found dead or dying collected by the SAGIR network are necropsied and when tularemia is suspected culture and/or PCR are performed to confirm the diagnosis. The aim of this study was to present the results of tularemia surveillance in wildlife and to investigate the spatial and temporal pattern of tularemia observed between the 2002-2003 and 2012-2013 hunting seasons in French wildlife. Fourty-one to 121 cases were collected each hunting season for a total of 693 confirmed cases and 46 additional suspected cases. The main species affected was the European Brown Hare (Lepus europaeus) but 4 rabbits (Oryctolagus cuniculus), 2 roe deer (Capreolus capreolus) and one wild boar (Sus scrofa) were also found positive. The Standard Mortality Ratio was mapped and Kulldorff's retrospective space-time scan statistic was implemented and allowed the detection of several clusters: the nationwide outbreak of 2007-2008; 2 clusters in northern and central-western France in high hare-abundance areas and another in Northeastern France where the abundance of hares is low. Our results confirm the usefulness of brown hare as a sentinel of environmental risk

Le parallélogramme au fil des cycles.: Des ressources pour les enseignants et les formateurs

National audienc

The Diversity Of Food Processes In Organic Short Chains The Case Of Artisanal Pasta

To provide local and healthy food, an increasing number of French farmers make the choice to not only produce cereals but also process them into flour or semolina, then pasta and sell them on farm or through local food networks. Less or no gluten sensitivity have been reported by some consumers of these handmade products. A current participatory project proposes to inventory such initiatives in Occitanie region, to describe their farming systems and to evaluate the quality of pasta. The first results showed that on-farm processing and marketing are mostly the fact of small-scale organic farms growing landraces durum wheat varieties and other orphan Triticum species. Stone-milling is mainly used instead of roller-milling and the pasta process is soft, simpler but longer than the industrial one. The raw materials and the final products were analyzed in order to understand how the process influences the final quality of pasta, particularly the gluten and organoleptic quality

Le parallélogramme au fil des cycles.: Des ressources pour les enseignants et les formateurs

National audienc

The diversity of food processes in organic short chains: the case of artisanal pasta

International audienceTo provide local and healthy food, an increasing number of French farmers make the choice to not only produce cereals but also process them into flour or semolina, then pasta and sell them on farm or through local food networks. Less or no gluten sensitivity have been reported by some consumers of these handmade products. A current participatory project proposes to inventory such initiatives in Occitanie region, to describe their farming systems and to evaluate the quality of pasta. The first results showed that on-farm processing and marketing are mostly the fact of small-scale organic farms growing landraces durum wheat varieties and other orphan Triticum species. Stone-milling is mainly used instead of roller-milling and the pasta process is soft, simpler but longer than the industrial one. The raw materials and the final products were analyzed in order to understand how the process influences the final quality of pasta, particularly the gluten and organoleptic quality

High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments.

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised

Quand l’innovation sociale réoriente l’innovation technologique dans les systèmes agroalimentaires : le cas des chaînes locales autour des blés

International audienceIn recent years, the technological lock-in of the wheat industry has led to the emergence of alternatives which are now taking on a new dimension with regard to consumer concerns about gluten. Based on a research-intervention in Occitanie and a national survey, this article proposes an interdisciplinary and systemic approach to the development of local wheat chains. It shows how farmers and artisans are carrying out social innovations that reorient technological innovation towards a new agri-food system taking into account new indicators of wealth. While taking part in the work on the scaling up of short food chains, it thus calls to study further the coupling between social innovation and technological innovation in the history and transition of agri-food systems.Le verrouillage technologique des filières blés a suscité, dans la période récente, l’émergence d’alternatives qui prennent aujourd’hui une nouvelle dimension au regard des préoccupations des consommateurs vis-à-vis du gluten. Basé sur une recherche-intervention en Occitanie et une étude menée à l’échelle nationale, cet article propose une approche interdisciplinaire et systémique du développement des chaînes locales autour des blés. Il montre comment des agriculteurs et des artisans portent des innovations sociales qui réorientent l’innovation technologique vers un nouveau système agroalimentaire prenant en compte de nouveaux indicateurs de richesse. Tout en prenant place dans les travaux sur le changement d’échelle des circuits courts alimentaires, il appelle ainsi à approfondir le couplage entre innovation sociale et innovation technologique dans l’histoire et la transition des systèmes agroalimentaires