The primary objective of this dissertation is to utilise, adapt and extend current stochastic models and statistical inference techniques to describe the transmission of nosocomial pathogens, i.e. hospital-acquired pathogens, and multiply-resistant organisms within the hospital setting. The emergence of higher levels of antibiotic resistance is threatening the long term viability of current treatment options and placing greater emphasis on the use of infection control procedures. The relative importance and value of various infection control practices is often debated and there is a lack of quantitative evidence concerning their effectiveness. The methods developed in this dissertation are applied to data of methicillin-resistant Staphylococcus aureus occurrence in intensive care units to quantify the effectiveness of infection control procedures. Analysis of infectious disease or carriage data is complicated by dependencies within the data and partial observation of the transmission process. Dependencies within the data are inherent because the risk of colonisation depends on the number of other colonised individuals. The colonisation times, chain and duration are often not visible to the human eye making only partial observation of the transmission process possible. Within a hospital setting, routine surveillance monitoring permits knowledge of interval-censored colonisation times. However, consideration needs to be given to the possibility of false negative outcomes when relying on observations from routine surveillance monitoring. SI (Susceptible, Infected) models are commonly used to describe community epidemic processes and allow for any inherent dependencies. Statistical inference techniques, such as the expectation-maximisation (EM) algorithm and Markov chain Monte Carlo (MCMC) can be used to estimate the model parameters when only partial observation of the epidemic process is possible. These methods appear well suited for the analysis of hospital infectious disease data but need to be adapted for short patient stays through migration. This thesis focuses on the use of Bayesian statistics to explore the posterior distributions of the unknown parameters. MCMC techniques are introduced to overcome analytical intractability caused by partial observation of the epidemic process. Statistical issues such as model adequacy and MCMC convergence assessment are discussed throughout the thesis. The new methodology allows the quantification of the relative importance of different transmission routes and the benefits of hospital practices, in terms of changed transmission rates. Evidence-based decisions can therefore be made on the impact of infection control procedures which is otherwise difficult on the basis of clinical studies alone. The methods are applied to data describing the occurrence of methicillin-resistant Staphylococcus aureus within intensive care units in hospitals in Brisbane and London

Production de bois et autres ressources (gibier, champignons,...), conservation de la biodiversité et gestion des paysages, la forêt a suscité de riches débats depuis quelques années, le Grenelle de l'Environnement ayant révélé des intérêts parfois contradictoires. Si le gestionnaire forestier tente de développer autant que possible une gestion multifonctionnelle de ses forêts, il reste dépendant des connaissances fragmentaires sur les interactions dans les écosystèmes forestiers. La politique actuelle, qui vise à concilier la production de bois et la préservation des espèces, repose plus sur des expériences de terrain que sur des études étayées scientifiquement. Les Chiroptères comptent des espèces candidates pour étudier l'influence de la gestion forestière sur la biodiversité : le jour, elles occupent des gîtes arboricoles et, la nuit, elles exploitent des habitats forestiers pour chasser leurs proies, qui dépendent elles-mêmes de micro-habitats forestiers. Pour aider le gestionnaire à mettre en œuvre une stratégie de gestion conservatoire, nous avons étudié l'utilisation des ressources de la forêt par trois espèces : Myotis bechsteinii, Myotis nattereri et Plecotus auritus. La radio-localisation a permis d'identifier des réseaux d'arbres-gîte dont l'occupation varie selon les espèces, leur statut reproducteur et l'implication dans le comportement de fission-fusion des colonies de parturition. Les différentes utilisations des gîtes impliquent une stratégie de gestion propre à chaque espèce, voire à chaque colonie de reproduction. Procurant a priori de potentiels gîtes et proies, le bois mort debout favorise la richesse spécifique des Chiroptères forestiers à partir de 25 m3 à l'hectare, mais une stratification de la végétation pourrait être un objectif de gestion, la réponse des espèces était essentiellement liée à la structure forestière des trouées induites par le bois mort. Ce travail a ensuite nécessité de s'intéresser aux méthodes permettant de comprendre l'utilisation de l'espace par chaque individu (domaine vital) et la façon dont chacun d'eux fréquente ses terrains de chasse (sélection de l'habitat). Compte tenu des limites technologiques, le Kernel semble actuellement la meilleure méthode de représentation et de calcul de surface du domaine vital alors que la K-select a livré des résultats significatifs pour mettre en évidence des facteurs de sélection d'habitat. Les surfaces des domaines vitaux et des centres d'activité varient selon les espèces, Myotis bechsteinii associe de petites surfaces à un comportement territorial, surtout en période d'allaitement. M. nattereri et Plecotus auritus peuvent exploiter de grands espaces sur lesquels ils se limitent à de petits centres d'activité. Les colonies de ces dernières pourront plus facilement se déplacer dans leur domaine vital au gré des itinéraires de gestion mis en œuvre. Les caractéristiques des habitats forestiers utilisés comme terrains de chasse varient selon les espèces, voire le sexe, l'âge et le statut reproducteur des individus, mais toutes trois montrent une forte sélectivité pour les peuplements forestiers présentant un fort encombrement végétal, des gros arbres et une forte structuration du peuplement. Cinq principes de gestion dans un contexte fort de production de bois sont développés en conclusion des résultats avec deux exemples de stratégies de gestion destinée au maintien des Chiroptères. / The forest is the center of many interests that fuel the debates of our society. These debates are particularly exacerbated since the french " Grenelle de l'Environnement " in 2008. Among the various expectations, forest produce wood that is the subject of attentions, both by an increased demand for certain types of trees and by the naturalist world which sees in it one of last refuges for biodiversity in our modified landscapes. Thus, if the forest manager is trying to develop a management that is as much multifunctional as possible, it remains dependent on fragmented knowledge on the link between biodiversity and the forest ecosystem. Despite the establishment of a conservation policy that seeks to balance timber production and species preservation, the way to conduct such a policy is based on concrete field experiences yet scientifically unsubstantiated. Bats are good candidate species to study the response of biodiversity to forest management: they select networks of tree-roosts in which they form breeding colonies composed of several dozen individuals and they exploit forest habitats to hunt their prey, prey which themselves depend on forest microhabitats. However, their study is recent in forest and provides very vague management guidelines. To help managers implement a conservation management strategy, we thus studied the behavior of forest usage by three species of gleaning bats, Myotis bechsteinii, Myotis nattereri and Plecotus auritus. This work required to focus on the methods available to understand the use of space by each individual (home range) and how each individual selects its hunting habitats. We showed that each species had a unique response to available habitats and that the status of individuals (sex, age and reproductive status) intervenes in explaining the selection of tree roosts and hunting grounds. Both compartments are constrained by the availability of suitable habitat, helping to explain the structuring of habitat selection factors and the shape and surface of individual home ranges. Furthermore, the way networks of tree-roost are used partly explains the types of roosts selected. These different results means that it is necessary to lay down specific management strategies for each species, even each breeding colony. Finally, we studied the role of deadwood to explain the presence of bats in forests. We have shown that species richness increased from standing deadwood of 25m3 per hectare, while the response of species to deadwood was mainly restricted to forest habitat structure produced by the gaps resulting from the deadwood patch, favoring particularly edge-foraging species. Some species do however clearly benefit from insects emerging from deadwood. Five recommendations are proposed for the conservation of these species in a context of strong wood production.