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Pathogen community composition and co-infection patterns in a wild community of rodents
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Supplementary data deposited in Zenodo (https://doi.org/10.5281/zenodo.7092812; Abbate et al., 2022) include the following 16S metabarcoding data: (i) raw sequence reads (fastq format), (ii) raw output files generated by the mothur program (iii) raw abundance table and (iv) filtered occurrence table, as well as (v) scripts and data files for statistical analyses. Items iii-v are also provided in Supplemental Materials Appendix 2 to directly accompany this publication.All procedures and methods were carried out in accordance with relevant regulations and official guidelines from the American Society of Mammalogists. All protocols presented here were realized with prior explicit agreement from relevant institutional committee (Centre de Biologie pour la Gestion des Populations, CBGP: 34 169 003).. International audience. Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.
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