CERoPath

WP1.1 Rodents and their pathogens: collection and identification

Murine rodents  will be collected in different localities characterized by their habitat complexity, and on the basis of the knowledge of recent environmental changes that may have impacted them (WP3). Rodents will be trapped by partners 1, 1a, 1b, 1d, 1e, 2, 2a, 5; and their organs and blood will be collected and stored according to well-established protocols. Relevant skeletal structures will be collected for estimating phenotypic effects of parasitic load / environmental deterioration / sympatry (WP2). If necessary, rodents will be identified by genetic markers (WP2) by partners 1, 2. Ectoparasites  (fleas, mites, ticks and lice) and endoparasites (helminths) will be collected, identified and stored by partners 1, 1a, 5. Pathogens will be revealed and identified by serology and PCR/sequencing: viruses  (hantaviruses, LCMV-group, poxviruses) by partners 1e and 7, bacteria  (Leptospira  spp. , Rickettsia  spp. Bartonella  spp.) by partners 1c, 7 and 8, protozoans  (Trypanosoma spp. Toxoplasma spp. ) by partners 1a and 7 and fungi  (Pneumocystis,  Penicillium marneffei ) by partner 6 using routine protocols [23].
 

WP1.2. Phylogenetics, phylogeography and molecular epidemiology

Molecular markers will be used to address ecological and microevolutionary processes in hosts and pathogens. These will include species identification, population genetic structure and phylogeography. A first objective is to improve preliminary results on the molecular phylogeny of South-East Asian rodents , extending our researches on a larger sampling and geographical range. These results will be compared with those obtained in morphometry (WP2) in order to define the best characters for species diagnosis. A second objective concerns the parasites and pathogens, where host specificity, identification of rodent reservoirs, modes of reproduction and transmission patterns will be assessed using molecular tools [19] [25]. A third objective is to study the co-phylogeographic structure of some rodent-pathogen association  using the methodology developed in [54], which showed a strong correlation between the phylogeographic structures of the host and those of its parasite. Co-evolution events [37], and comparison of rate of molecular evolution in both the host and the parasite allow to identify local adaptation, undetected historical events like host switches or diversification [48] [53] [54], and potential geographic distribution of genetic lineages of its parasites. This information is particularly important on the epidemiological point of view to estimate the distribution range of strains of parasites and pathogens (in relation to WP4).

WP1.3. Patterns of hosts and pathogens assemblages

Patterns of host-pathogen association, nestedness, co-occurrence, (which rodent species is infected by which parasite species or pathogen strains in which locality) will be investigated using methodological tools of community ecology such as null models [30] [31] [39] [52] [62]. Specific attention will be paid to the role of host population structure in shaping the parasite communities [11].

Invariant scaling properties in host-pathogen webs will be investigated through the study of connectance [40]. The finding of such self-organizing principles would suggest that apparently diverse and idiosyncratic assemblages may possess common rules. At the opposite, an absence of constant connectance through space and time would suggest that environmental and/or human-based disturbances may modify host-pathogen relationships and may decrease their predictability. In this case the challenge will be to identify the processes underpinning any differences in host-pathogen assemblage structures which in turn would provide crucial knowledge allowing advances in conservation and environmental management.

Specific outputs regarding this WP1

  1/ enhancement of rodents and pathogens identifications, identification of host reservoirs

  2/ phylogenies and phylogeographic studies of selected rodent species: both commensal and wild (Mus spp., Bandicota spp., Rattus spp.) and wild (Maxomys  spp, Leopoldamys spp., Niviventer  spp.)

  3/ molecular epidemiology of selected parasites and pathogens. In first attempts, we will focus on hantaviruses, LCMV-group, pox viruses Leptospira spp, Rickettsia spp., Pneumocystis  spp. and chigger mites

  4/ patterns of assemblages of interactive communities.