Résumé
Pathogens actually share host plants with a myriad of other microbes, some of them being pathogenic. Multiple infections, or ‘co-infection’, occur when a single host plant is infected by various pathogen species, or genotypes. This is known to affect symptom expression and pathogen multiplication in various pathosystems. However, the population-scale consequences remain poorly explored, and this will be discussed in the introduction, focusing on evolutionary and epidemiological consequences of multiple infections.I will then illustrate by our work (IRD-INERA-PathoBios team) on rice diseases in Burkina Faso. Through a multi-pathogen epidemiological survey, we documented the dynamics of various rice diseases jointly. Symptom monitoring annually at the same developmental stage showed that rice blast, and bacterial leaf streak (BLS) disease, were preferentially found in irrigated areas, compared to rainfed lowlands. High levels of co-occurrences were found between the four rice diseases under study, particularly in irrigated areas. The rice yellow mottle disease, due to the RYMV, is not affected by the rice production system, but instead by the specific site. A very high genetic diversity for RYMV, with the co-occurrence of four distinct lineages, at the small geographical scale of one irrigated perimeter identified as a disease hotspot. Temporal dynamics suggest an evolution of the relative frequencies of each genetic lineage within the studied period, and differences between isolates in terms of viral load estimated under controlled condition may contribute to explain observed RYMV population evolution.Finally, we focused on the RYMV and the bacteria causing BLS to investigate the evolutionary consequences of multiple infections, with potential impact on epidemiology, because these two pathogens were shown to interact reciprocally in experimental co-infection. Preliminary results of this ongoing project show high levels of mixed infections by various RYMV isolates, and in one site, a different RYMV population composition between viral mono-infection and virus-bacteria co-infection. Overall, I will discuss how multiple infections impact the evolutionary trajectories of pathogen populations and drive epidemiological outcome.