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Background  Canine brucellosis, due to  Brucella canis,  is a worldwide zoonosis that remains endemic in South America, including Brazil. Implementation of powerful whole-genome sequencing approaches allowed exploring the  Brucella  genus considered as monomorphic, with, to date, more than 500 genomes available in public databases .  Nevertheless, with under-representation of  B. canis  genomes −only twenty complete or draft genomes−, lack of knowledge about this species is still considerable. This report describes a comparative genomics-based phylogeographic investigation of 53  B. canis  strains, including 28 isolates paired-end sequenced in this work.    Results  Obtained results allow identifying a SNP panel species-specific to  B. canis  of 1086 nucleotides. In addition, high-resolution analyses assess the epidemiological relationship between worldwide isolates. Our findings show worldwide strains are distributed among 2 distinct lineages. One of them seems to be specific to South American strains, including Brazil.  B. canis  South American strains may be identified by a SNP panel of 15 nucleotides, whereas a 22 SNP panel is sufficient to define contamination origin from Brazil. These results lead to the proposal of a possible spread route for dog brucellosis through South America. Additionally, whole-genome analyses highlight the remarkable genomic stability of  B. canis  strains over time and the sustainability of the infection in São Paulo over 12 year-period.    Conclusions  Significant increase of  B. canis  genomes available in public databases provides new insights into  B. canis  infection in South America, including Brazil, as well as in the world, and also offers new perspectives for the  Brucella  genus  largo  sensu.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5001-6) contains supplementary material, which is available to authorized users.

New insights into phylogeography of worldwide Brucella canis isolates by comparative genomics-based approaches: focus on Brazil