Section: Ecology
Topic: Ecology, Microbiology, Population biology

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

10.24072/pcjournal.370 - Peer Community Journal, Volume 4 (2024), article no. e14.

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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 BartonellaMycoplasma 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.

Published online:
DOI: 10.24072/pcjournal.370
Type: Research article
Keywords: 16S rRNA amplicon high throughput sequencing, Disease Ecology, Microbial Interactions, Pathobiome, Rodent reservoirs, Zoonoses

Abbate, Jessica L. 1, 2, 3, 4; Galan, Maxime 1; Razzauti, Maria 1; Sironen, Tarja 5; Voutilainen, Liina 6; Henttonen, Heikki 6; Gasqui, Patrick 7; Cosson, Jean-François 1, 8; Charbonnel, Nathalie 1

1 CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
2 UMR MIVEGEC, IRD, CNRS, Univ Montpellier, Montpellier, France
3 UMR UMMISCO, IRD, UPMC, UMI, Bondy, France
4 Geomatys, Montpellier, France
5 Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
6 Natural Resources Institute Finland (LUKE), FI-00790 Helsinki, Finland
7 UMR EPIA, INRAE, VetAgro Sup, Theix, France
8 UMR BIPAR, ENVA, INRAE, ANSES, Maisons-Alfort, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Abbate, Jessica L. and Galan, Maxime and Razzauti, Maria and Sironen, Tarja and Voutilainen, Liina and Henttonen, Heikki and Gasqui, Patrick and Cosson, Jean-Fran\c{c}ois and Charbonnel, Nathalie},
     title = {Pathogen community composition and co-infection patterns in a wild community of rodents},
     journal = {Peer Community Journal},
     eid = {e14},
     publisher = {Peer Community In},
     volume = {4},
     year = {2024},
     doi = {10.24072/pcjournal.370},
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%A Galan, Maxime
%A Razzauti, Maria
%A Sironen, Tarja
%A Voutilainen, Liina
%A Henttonen, Heikki
%A Gasqui, Patrick
%A Cosson, Jean-François
%A Charbonnel, Nathalie
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Abbate, Jessica L.; Galan, Maxime; Razzauti, Maria; Sironen, Tarja; Voutilainen, Liina; Henttonen, Heikki; Gasqui, Patrick; Cosson, Jean-François; Charbonnel, Nathalie. Pathogen community composition and co-infection patterns in a wild community of rodents. Peer Community Journal, Volume 4 (2024), article  no. e14. doi : 10.24072/pcjournal.370.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.ecology.100087

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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