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Here, we describe for the first time the prevalence and genetic properties ofBartonella organisms in wild rodents in Japan. We captured 685 wild rodents throughout Japan (in 12 prefectures) and successfully isolatedBartonella organisms from 176 of the 685 rodents (isolation rate, 25.7%). ThoseBartonella isolates were all obtained from the rodents captured in suburban areas (rate, 51.8%), but no organism was isolated from the animals captured in city areas. Sequence analysis ofrpoB andgltA revealed that theBartonella isolates obtained were classified into eight genetic groups, comprising isolates closely related toB. grahamii (A-I group),B. tribocorum andB. elizabethae (B-J group),B. tribocorum andB. rattimassiliensis (C-K group),B. rattimassiliensis (D-L group),B. phoceensis (F-N group),B. taylorii (G-O group), and probably two additional novelBartonella species groups (E-M and H-P).B. grahamii , which is one of the potential causative agents of human neuroretinitis, was found to be predominant in Japanese rodents. In terms of the relationships between theseBartonella genetic groups and their rodent species, (i) the A-I, E-M, and H-P groups appear to be associated withApodemus speciosus andApodemus argenteus ; (ii) the C-K, D-L, and F-N groups are likely implicated inRattus rattus ; (iii) the B-J group seems to be involved inApodemus mice andR. rattus ; and (iv) the G-O group is probably associated withA. speciosus andClethrionomys voles. Furthermore, dual infections with two different genetic groups of bartonellae were found inA. speciosus andR. rattus . These findings suggest that the rodent in Japan might serve as a reservoir of zoonoticBartonella infection.

Prevalence and Genetic Diversity of Bartonella Species Isolated from Wild Rodents in Japan