Maria Razzauti | Search bioRxiv

bioRxiv2016

Microevolution of Bank Voles (Myodes glareolus) at Neutral and Immune Related Genes During Multiannual Dynamic Cycles: Consequences for Puumala hantavirus Epidemiology

Understanding how host 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 immune-related genes involved in susceptibility to PUUV (Tnf-promoter, Mhc-Drb, 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 Mhc-Drb haplotypes and PUUV serology, and between Mx2 genotype and PUUV genogroups. These results show that microevolutionary changes and PUUV epidemiology in this metapopulation are mainly driven by neutral processes, although the relative effects of neutral and adaptive forces could vary temporally with density fluctuations.

Evolutionary Biology↗

bioRxiv2016

16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection

ImportanceSeveral recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. Rodents are intermediate hosts for numerous zoonotic bacteria. High-throughput sequencing (HTS) technologies are very useful for the detection and surveillance of zoonotic bacteria, but rigorous experimental processes are required for the use of these cheap and effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw dataset that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as bacterial positivity, prevalence and coinfection, by 16S rRNA amplicon sequencing on the MiSeq platform. This procedure, applied to 711 commensal rodents collected from 24 villages in Senegal, Africa, detected several emerging bacterial genera, some in high prevalence, while never before reported for West Africa. This study constitutes a step towards the use of HTS to improve our understanding of the risk of zoonotic disease transmission posed by wildlife, by providing a new strategy for the use of HTS platforms to monitor both bacterial diversity and infection dynamics in wildlife. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.\n\nSummaryHuman impact on natural habitats is increasing the complexity of human-wildlife interfaces and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential of recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of large numbers of samples, to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to eliminate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a trimming strategy for managing them and cleaning the dataset. We also analyzed 711 commensal rodents collected from 24 villages in Senegal, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis and 221 Mastomys erythroleucus. Seven major genera of pathogenic bacteria were detected: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus and Orientia. The last five of these genera have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90%, depending on the bacterial taxon, rodent species and site considered, and a mean of 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is, thus, particularly suitable for continuous pathogen surveillance in the framework of disease monitoring programs

Microbiology↗