Comparative genome analysis of Corynebacterium ulcerans isolates obtained in Japan

Corynebacterium ulcerans is a zoonotic pathogen that causes infections in humans that are clinically indistinguishable from those caused by Corynebacterium diphtheriae. In many developed countries, including Japan, companion animals such as dogs and cats are the predominant source of C. ulcerans infection. To date, we have collected 106 Japanese clinical and domestic animal isolates of C. ulcerans and a recently branched species, Corynebacterium ramonii, most of which were isolated from humans and cats. In the present study, we performed a comparative analysis of whole-genome sequences from 106 Japanese isolates in our collection and from 597 published isolates, both from Japan and from outside Japan. The Japanese isolates were divided into two distinct lineages: C. ulcerans and C. ramonii. The multilocus sequence types (MLST) of C. ulcerans Japanese isolates exhibited a unique distribution pattern, with one major type (ST 337) accounting for 69.0%, which is very rare in Europe. In addition to Japan, distinct MLST pattern compositions were observed across geographically distinct regions. The sequence types were associated with lysogenized prophage types that encode the diphtheria toxin (tox) gene and were partially associated with toxin production under certain conditions. Through single nucleotide variant (SNV) analysis, transmission from animals to humans has been suggested in some clinical cases.IMPORTANCEA large-scale genome analysis of Corynebacterium ulcerans in Europe has recently been reported, but not yet in Asia. By comparing the genomes of Japanese and European isolates, we demonstrate striking geographic differences in multilocus sequence types and toxigenic prophage compositions between these globally different areas. Notably, we identify the predominance of sequence type ST 337 in Japan. This lineage is rare in Europe and shows that prophage types encoding the diphtheria toxin are closely associated with specific sequence types and toxin production phenotypes. Our single-nucleotide variant analyses further provide genomic evidence supporting zoonotic transmission between companion animals and humans in several clinical cases.