Ecologie de la résistance aux anbiotiques de Escherichia coli et Staphylococcus aureus dans les flores commensales de l'homme et des animaux en milieu naturel. Transition vers la virulence et impact sur la santé humaine – ANR-05-SEST-0017

Background. Bacterial resistance to antibiotics is a major public health problem worldwide. The commensal flora of humans constitutes a major reservoir of potentially pathogenic bacteria and resistance genes. The level of resistance depends on the selective antibiotic pressure in the source population, and on the latter’s diet, environment and hygiene. The characteristics of this reservoir may affect those of (i) the bacteria that cause infections in humans and (ii) the bacteria that populate the commensal flora of the local animal species, according to a gradient whose intensity decreases with distance. Objectives 1-To describe concomitantly the genomic characteristics of the resistance, phylogeny and virulence of the E. coli and S. aureus strains colonizing individuals living in a well-delineated geographical area, which has few contacts with the outside world and a single source of selective antibiotic pressure. 2- To compare these characteristics with those of (i) isolates causing human infections, and (ii) isolates colonizing the domestic and wild animals living nearby or further away, and the aqueous environment. To infer, for the E. coli and S. aureus strains, the ecological and genomic relationships between the human resistant commensal isolates, those causing infections, and those colonizing domestic or distant animals and the aqueous environment. Methods. We shall take advantage of the unique opportunity offered by the characteristics of the Amerindian Wayampi villages of 3-Sauts on the Oyapock river (French Guiana), where there is a single source of selective antibiotic pressure, because of the isolated position of these villages in the middle of the tropical forest, the traditional way of life and diet of the villagers, and the presence of a health officer who manages all the deliveries of antibiotics and organises all medical transport outside the village. For one year, E. coli urinary-tract and intestinal infections, and S. aureus cutaneous infections, will be under continuous surveillance and the isolates saved. Two sampling campaigns will be conducted, during the dry and rainy seasons, respectively and specimens of the following will be collected of the commensal flora of (i) the villagers (nostrils, and stools), (ii) domestic pigs, chickens, and dogs (nostrils, and faeces), (iii) nearby wild rodents, marsupials and bats (nostrils, and faeces, by the transect method) and (iv) the river waters upstream and downstream the villages. Specimens will be frozen for isolation of E. coli and S. aureus strains. The isolates will be characterized and compared in the laboratories of the investigators. Intestinal colonization with yeasts will also be investigated as a surrogate marker of post-antibiotic ecological disturbances. Expected results. The results are expected (i) to confirm or refute the current hypotheses concerning the ecological relationships between resistant E. coli and S. aureus isolates from human commensal flora, local animal species, and the aqueous environment, and (ii) to enable us to describe the ecological and genomic conditions of the emergence of virulence, by comparing the isolates of commensal flora to the isolates respectively causing urinary, intestinal, and cutaneous infections in humans.