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L'occupation quasi constante des environnements intérieurs (en moyenne 90% du temps), expose en permanence les occupants à une large variété de microorganismes présents dans l'air de ces espaces. En raison de difficultés technologiques liées à la collecte et à l'analyse, ce domaine scientifique reste pourtant quasiment vierge et ce, malgré les retombées possibles dans le domaine de la santé. Le manque est particulièrement marqué, en ce qui concerne l'exposition des individus aux aérosols microbiens et plus globalement la gestion sanitaire de la qualité de l'air des espaces clos. Cette étude a pour objectif la caractérisation de la diversité microbienne de l'air de différents espaces clos collectifs par une approche qualitative et quantitative. L'ensemble de l'étude a porté sur des environnements sensibles d'un point de vue des occupants (Hôpital), de la densité de fréquentation (Le Musée du Louvre) ou d'un temps d'exposition prolongé (Bureau).L'originalité de cette thèse a résidé dans l'association d'une stratégie d'échantillonnage représentative des environnements étudiés et d'outils analytiques pertinents permettant d'étudier la microflore de l'air indépendamment de la cultivabilité des micro-organismes. Pour la première fois, un séquençage haut débit (pyroséquençage 454) a été appliqué à des échantillons d'air intérieur permettant d'accéder à une diversité microbienne rare comme le sont les espèces pathogènes. Les résultats montrent une diversité microbienne plus riche que celle habituellement observée par des méthodes culturales. Plusieurs micro-organismes impliqués dans des problématiques sanitaires ont été retrouvés (Borrelia spp., Burkholderia spp., Legionella spp., Neisseria spp. et Mycobacterium spp.). Les résultats mettent en évidence une stabilité à la fois spatiale et temporelle pour les bactéries retrouvées dans l'air intérieur. Cette stabilité est à la fois qualitative (structure des communautés microbiennes) et quantitative (abondance des microorganismes). La forte présence de séquences d'origine humaine permet de considérer l'Homme comme le principal élément orientant la microflore bactérienne de l'air intérieur. Des « cores species » signant l'air intérieur anthropisé ont pu être identifiées. / The constant occupation of indoor environments (average 90% of the time), constantly confront the occupants to a wide variety of microorganisms from the air of these spaces. Due to technological difficulties related to the collection and the analysis of airborne microorganisms, this field of study remains scanty, despite the potential health impact. The lack is particularly pronounced in terms of understanding of the risks of contamination of people by bioaerosols and overall health management of air quality of confined spaces.This study aims to characterize dynamics of the microbial diversity of different indoor environments. The entire study involved representative environments (hospital, office and museum).The originality of this thesis is the combination of a representative sampling strategy on environments studied and of analytical tools relevant to study the microflora of the indoor air regardless of the culturability of microorganisms.. For the first time, a high throughput sequencing (454 pyrosequencing) was applied to samples of indoor air in order to assess microbial diversity and pathogenic species..Several microorganisms implicated in health problems were found (Borrelia spp., Burkholderia spp. ,Legionella spp., Neisseria spp. and Mycobacterium spp.).The results give a different and more varied qualitative picture than that usually observed by cultural methods. The results show a stability of both spatial and temporal microflora of indoor air. This stability is both qualitative (microbial community structure) and quantitative (abundance of microorganisms). Man can be considered as the main factor driving the indoor air microflora due to the strong presence of sequences of human origin.'Cores species' signing the antropogenic indoor air were identified.

Microbial pathogens commonly transmitted through the aerosol route to surfaces, equipment, and hands in the clinical setting leads to costly and life threatening hospital-acquired infections (HAIs). Even with improved hand hygiene and surface disinfection, HAIs continue to persist in healthcare environments, warranting consideration of novel interventions to reduce the transmission risk of HAIs. This study quantitated the efficacy of ion generating passive air treatment (PAT) against viruses (MS2), bacteria (Escherichia coli), and bacterial spores (Bacillus thuringiensis) in a controlled environmental setting. Microorganisms were seeded into a 2.72 m3 chamber using a positive pressure nebulizing device to generate aerosolized droplets. The PAT unit was then turned on and seeded organisms were collected at various time points using impingers to concentrate the organisms into sterile aqueous solution. The microorganisms were enumerated using approved standard protocols developed in the Environment, Exposure Science, and Risk Assessment Center's laboratory at The University of Arizona. Three experiments were conducted to challenge the PAT unit. Experiment one evaluated the efficacy of the PAT unit over a single 10-minute period on microbial inactivation from the airborne environment following a single seeding; additionally, experiment one aimed to determine the efficacy of the PAT unit against viruses, bacteria, and bacterial spores on environmental surfaces; experiment two evaluated the efficacy of the PAT unit running continuously over a period of 6 hours following a single seeding; and experiment three evaluated the efficacy of the PAT unit running two continuously over a period of 5.25 hours following two seeding events. Bacterial spores from pre- and post-treatment with the PAT unit were collected and analyzed by scanning electron microscopy to assess structural differences. After a single seeding and 10 minutes of continuous treatment of the PAT unit, normalized average microbial log10 reductions of post-treatment compared to pre-treatment air concentrations were 1.67, 0.59, and 1.04 for MS2, B. thuringiensis spores, and E. coli, respectively. Differences in average log10 reductions between the control unit and the PAT unit were statistically significant for MS2 (p=0.009) and B. thuringiensis (p=0.0455), but not for E. coli (p=0.0565). The geometric mean log10 surface concentrations of MS2, B. thuringiensis, and E. coli after a single seeding and 10 minutes of continuous treatment of the PAT unit were 7.30 PFU/100 cm2, 5.90 CFU/100 cm2, and 2.74 CFU/100 cm2, respectively, compared to exposure of the control unit, 8.59 PFU/100 cm2, 6.03 CFU/100 cm2, and 4.96 CFU/100 cm2, respectively. There was a statistically significant difference between the mean log10 surface concentrations following 10 minutes of treatment with the control unit compared to the PAT unit for E. coli (p=0.002), but not for MS2 (p=0.3358) or B. thuringiensis (p=0.0866). After a single seeding and 6-hours of continuous treatment of the PAT unit, normalized average microbial log10 reductions of MS2 and B. thuringiensis were 1.43 and 1.32, respectively. The difference in average log10 reduction of all post-treatment samples between the control unit and the PAT unit was statistically significant for B. thuringiensis (p=0.0008) but not for MS2 (p=0.2568). After two seedings and 5.25 hours of continuous treatment of the PAT unit, normalized average microbial log10 reductions of MS2 and B. thuringiensis were 1.59 and 1.26, respectively. There was a statistically significant difference in the average log10 reductions between the control unit and the PAT unit for MS2 (p=0.002) and B. thuringiensis (p=0.0003). Scanning electron microscopy analysis identified visual modification to B. thuringiensis spores following treatment with the PAT unit. In this study, the tested ion generating PAT unit was effectively able to reduce airborne microbial concentrations between 1-2 log10 in a controlled chamber environment within 10 minutes and up to 6 hours of treatment. The implications of this study suggest that ion producing PAT systems may represent a beneficial supplement to cleaning and disinfection practices in the reduction of pathogen contamination from the airborne and fomite-airborne routes.