Molecular characterization and ultrastructure of a new amoeba endoparasite belonging to the Stenotrophomonas maltophilia complex

► Free-living amoebae may harbor potential pathogenic organisms as endosymbionts. ► Naegleria and Acanthamoeba were recovered being infected by endoparasitic bacteria. ► Endoparasites grow only within some amoebae, not onto bacteriological media. ► Phylogenetic analysis identifies endoparasites as Stenotrophomonas maltophilia. ► First case of the opportunistic pathogen S. maltophilia as obligate amoeba endoparasite.