Dispersal in [i]Mastomys natalensis[/i] mice: use of fine-scale genetic analyses for pest management

Mastomys natalensis is the major pest rodent in sub-Saharan Africa. In this study, population genetic techniques were used to gain new insights into its dispersal behaviour, a critical parameter in pest management. Using 11 microsatellites, 272 individuals from a 300 ha area in Tanzania were genotyped. Genetic diversity was high, with no isolation by distance and little differentiation between field plots far apart, indicating a large effective population size and high dispersal rates in agreement with ecological observations. On the other hand, genetic differentiation between nearby field plots, isolation by distance within a single field plot and kin clustering were also observed. This apparent contradiction may be explained by yearly founder effects of a small number of breeding individuals per square area, which is consistent with the presence of linkage disequilibrium. An alternative, not mutually exclusive explanation is that there are both dispersing and sedentary animals in the population. The low-density field plots were characterized by low relatedness and small genetic distances to other field plots, indicating a high turnover rate and negative density-dependent dispersal. In one field plot female-biased dispersal was observed, which may be related to inbreeding avoidance or female competition for resources. Most juveniles appeared to be local recruits, but they did not seem to stay in their native area for more than two months. Finally, possible implications for pest management are discussed

Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife

Background Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq) and 16S-metagenomics, assessing their ability to survey neglected zoonotic bacteria in rodent populations.Methodology/Principal Findings : We first extracted nucleic acids from the spleens of 190 voles collected in France. RNA extracts were pooled, randomly retro-transcribed, then RNA-Seq was performed using HiSeq. Assembled bacterial sequences were assigned to the closest taxon registered in GenBank. DNA extracts were analyzed via a 16S-metagenomics approach using two sequencers: the 454 GS-FLX and the MiSeq. The V4 region of the gene coding for 16S rRNA was amplified for each sample using barcoded universal primers. Amplicons were multiplexed and processed on the distinct sequencers. The resulting datasets were de-multiplexed, and each read was processed through a pipeline to be taxonomically classified using the Ribosomal Database Project. Altogether, 45 pathogenic bacterial genera were detected. The bacteria identified by RNA-Seq were comparable to those detected by 16S-metagenomics approach processed with MiSeq (16S-MiSeq). In contrast, 21 of these pathogens went unnoticed when the 16S-metagenomics approach was processed via 454-pyrosequencing (16S-454). In addition, the 16S-metagenomics approaches revealed a high level of coinfection in bank voles. Conclusions/Significance :We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each individual reservoir, with subsequent derivation of bacterial prevalence in host populations, and generation of intra-reservoir patterns of bacterial interactions. Lastly, the number of bacterial reads obtained with the 16S-MiSeq could be a good proxy for bacterial prevalence

Microevolution of bank voles (Myodes glareolus) at neutral and immune-related genes during multiannual dynamic cycles : Consequences for Puumala hantavirus epidemiology

Understanding howhost dynamics, including variations of population size and dispersal, may affect the epidemiology of infectious diseases through ecological and evolutionary processes is an active research area. Here we focus on a bank vole (Myodes glareolus) metapopulation surveyed in Finland between 2005 and 2009. Bank vole is the reservoir of Puumala hantavirus (PUUV), the agent of nephropathia epidemica (NE, a mild form of hemorrhagic fever with renal symptom) in humans. M. glareolus populations experience multiannual density fluctuations that may influence the level of genetic diversity maintained in bank voles, PUUV prevalence and NE occurrence. We examine bank vole metapopulation genetics at presumably neutral markers and immunerelated genes involved in susceptibility to PUUV (Tnf-promoter, Tlr4, Tlr7 and Mx2 gene) to investigate the links between population dynamics, microevolutionary processes and PUUV epidemiology. We show that genetic drift slightly and transiently affects neutral and adaptive genetic variability within the metapopulation. Gene flow seems to counterbalance its effects during the multiannual density fluctuations. The low abundance phase may therefore be too short to impact genetic variation in the host, and consequently viral genetic diversity. Environmental heterogeneity does not seem to affect vole gene flow, which might explain the absence of spatial structure previously detected in PUUV in this area. Besides, our results suggest the role of vole dispersal on PUUV circulation through sex-specific and density-dependent movements. We find little evidence of selection acting on immune-related genes within this metapopulation. Footprint of positive selection is detected at Tlr-4 gene in 2008 only. We observe marginally significant associations between Mx2 genotype and PUUV genogroups. These results show that neutral processes seem to be the main factors affecting the evolution of these immune-related genes at a contemporary scale, although the relative effects of neutral and adaptive forces could vary temporally with density fluctuations. Immune related gene polymorphism may in turn partly influence PUUV epidemiology in this metapopulation. (C) 2016 Published by Elsevier B.V.Peer reviewe

Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.Peer reviewe

Concomitant influence of helminth infection and landscape on the distribution of Puumala hantavirus in its reservoir, Myodes glareolus

Peer reviewe

Pathogen discovery, large-scale screening, pathobiome characterisation and highlighting of interaction between microorganisms (and effect on transmission)

National audienc

Genetic structure and population dynamics in a landscape context

International audienceThe recognition that landscape features influence the distribution of genetic variability, as well as the intensity and the direction of gene flow, has prompted the development of a new discipline (landscape genetics), which is now well-established within the scientific community. Here, we briefly present the main theoretical aspects that allow using the analysis of genetic variability as surrogates of population dynamics and dispersal. We describe common statistical approaches developed in the context of landscape genetics. Finally, we illustrate the contribution of landscape genetics to better understanding of the dynamics of fluctuating rodent populations and some complex phenomena such as travelling waves. We also document the use of landscape genetics to understand the circulation of rodent-borne pathogens and their distribution within landscapes. This knowledge illustrates the potential contribution of landscape genetics to the understanding the ecological processes occurring within rodent populations at the landscape scale

Molecular epidemiology of disease resistance genes with perspectives for researches on biological invasions and hybrid zones

International audienceMolecular epidemiology has largely been investigated from the parasite side, therefore contributing to a better understanding of transmission patterns and factors influencing disease spread. From the hosts’ point of view, molecular epidemiology has lead to the identification of components of susceptibility and resistance to infectious diseases. In this chapter, we aim to explain why resistance to infections exhibits such a remarkable degree of polymorphism while being resistant obviously confers a high selective advantage to hosts. In this context, we develop host molecular epidemiology with regard to the concepts of evolutionary biology and immunoecology. We detail the mechanisms that are likely to underlie the variable degrees of host resistance polymorphism observed among natural populations. Particular attention is given to recently emphasized topics, including the risks of immunopathology, the spatial structure of populations, the impact of neutral evolutionary processes and the phenotypic plasticity of resistance. We evidence the consequences of this polymorphism for disease epidemiology both from empirical examples and genetic epidemiological modelling of resistance evolution. We stress the numerous gaps that remain to be explored to understand these patterns of disease resistance polymorphism. We particularly emphasize the cruel lack of theoretical predictions and data that have focused on biological invasions and hybridisation, two biological situations of main interest for emergenc

Maladie de Lyme. Les tiques, leurs hôtes & les agents infectieux

Débats avec citoyenNational audienc

Social relationships in Mastomys huberti as deduced from field and genetic analyses of multiple capture data

International audienceMultiple captures (i.e., the simultaneous capture of two or more individuals in the same trap) in rodent populations provide useful information on their social structure. Adding genetic analyses to these data enables to describe social links between individuals at a finer level. Here, we analyze the distribution and composition of multiple captures obtained during a 3-year study of a population of the murid rodent Mastomys huberti in Mali. In total, 133 multiple captures were recorded, representing more than 17% of the total number of individual capture events. Seasonal variations in the incidence of multiple captures were observed, and the young (classified as juveniles or subadults) were involved in multiple captures more often than expected. Juveniles (<21 g) were captured together more often than expected, suggesting that they usually forage in groups. This trend was also observed in subadults (<31 g), accompanied by a clear deficit of captures involving one subadult and one adult of the same sex, especially in males. This pattern could illustrate a phase when negative intraspecific interactions occur, possibly linked to dispersal of subadult males. Genotypic characterization of a significant fraction of the population using 11 microsatellite loci enabled to show that individuals caught together were significantly more closely related than those involved in single captures, even when close from each other. A seasonal trend of relatedness of these co-captured animals was also confirmed