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Mosquitoes are the main vectors of pathogens affecting wild animals, livestock and humans. Here, we used molecular tools to assess the local circulation of filarial parasites in mosquitoes collected during 2013 from natural, rural and urban habitats from southern Spain. We screened parasites in 22,791 female mosquitoes of the genera Aedes, Culex and Culiseta. Filarial worms were only detected in two mosquito pools. An Ae. caspius pool was positive for Setaria equina and an unidentified worm related to Onchocerca was detected in a Cx. pipiens pool. None of the mosquito pools were positive for Dirofilaria. These results underlay the role of Ae. caspius in the transmission of Setaria parasites among livestock and/or wildlife to humans in southern Spain.

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