Pathogen community composition and co-infection patterns in a wild community of rodents

Abstract

21Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is 22 therefore important to know what pathogens naturally circulate in rodent populations, and to 23 understand the factors that may influence their distribution in the wild. Here, we describe the 24 incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among 25 rodent communities in northern France. The community sample consisted of 713 rodents, including 26 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, 27 cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody 28 assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic 29 samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses 30 were used to determine the degree to which extrinsic factors contributed to pathogen community 31 structure, and to identify patterns of associations between pathogens within hosts. We found a rich 32 diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host 33 species is the most important determinant of pathogen community composition, and that hosts that 34 share habitats can have very different pathogen communities. Pathogen diversity and co-infection 35 rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases 36 suggests that some rodent species may be more important for transmission risk than others. 37Moreover we detected positive associations between several pathogens, including Bartonella, 38Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally 39 specific to particular host species. Altogether, our results suggest that host and pathogen specificity 40 is the most important driver of pathogen community structure, and that interspecific pathogen-41 pathogen associations also depend on host species. 42 43

Serological evidence of single and mixed infections of Rift Valley fever virus, Brucella spp. and Coxiella burnetii in dromedary camels in Kenya

“…This is especially true for livestock in pastoral communities in Sub-Saharan Africa with no structured disease control programs, a consequence of which is continuous exposure to endemic pathogens [ 18 , 59 ]. Extrinsic (environmental) and intrinsic (host-specific) factors influence burden and consequence of co-infections, but these are poorly understood for most endemic livestock diseases in sub-Saharan Africa [ 59 , 60 ]. Although the outcomes of in vivo pathogen interactions are poorly understood, it is known co-infections can result in change in severity of infection, alteration of transmission dynamics and variation in physiologic response which can change effectiveness of diagnostic techniques, control and prevention efforts [ 18 , 53 , 61 , 62 ].…”

Impact of Landscape on Host–Parasite Genetic Diversity and Distribution Using the Puumala orthohantavirus–Bank Vole System

“…The genetic pattern of a particular emerging parasite species will largely depend on the host dispersal and the overall host population dynamics [ 15 ]. Hence, host specificity is expected to have a strong impact on the distribution, the prevalence, and the genetic diversity of their parasites [ 92 ]. In particular, habitat preferences and population dynamics of the host should shape the local prevalence and the genetic diversity of its host-specific parasite.…”

Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations

“…We next described the presence/absence of pathogenic and zoonotic bacteria from the spleen of each bank vole. This lymphoid organ filters microbial cells in mammals and as such, enables to recover recent infections (Abbate et al ., In_revision; Diagne et al ., 2017). Molecular protocols, bioinformatics pipelines and data filtering were similar to those described above (gut bacteriome), except for the DNA extraction from splenic tissue using DNeasy 96 Tissue Kit (Qiagen).…”

“…Here, we strived to bridge these gaps by assessing the variability of gut bacteriome diversity and composition in wild populations of the bank vole Myodes glareolus , a small mammal reservoir of a large number of zoonotic agents (e.g., Abbate et al ., In_revision). We studied the relationships between its gut bacteriome, parasite infracommunities – focusing on gastro-intestinal helminths and pathogenic bacterial infections –, and host and environmental factors that may either influence or indicate the health status (e.g., proxies such as the body mass index (BMI)).…”