Comparative Genomic Analysis Reveals the Emergence and Dissemination of Different <i>Salmonella enterica</i> serovar Gallinarum biovar Gallinarum Lineages in Brazil

<i>Salmonella enterica</i> serovar Gallinarum biovar Gallinarum is a pathogenic bacterium that causes fowl typhoid (FT), affecting chicken flocks worldwide. This study aimed to evaluate the emergence, dissemination and genomic profile of <i>S.</i> Gallinarum lineages from Brazil. Twelve whole-genomes sequences (WGS) of different <i>S</i>. Gallinarum strains isolated from Brazilian poultry farms (2014 to 2018) were obtained and used to construct a dataset with other 31 previously published data (five more from Brazil). Brazilian strains phylogenetic diversity, temporal evolution and antimicrobial resistance/virulence genomic profile were evaluated. Sixteen (94.1%) Brazilian strains were from sequence type ST78 and one (5.9%) was from ST331. All <i>S.</i> Gallinarum strains clustered into five different clades/lineages (I to V), all circulating in South America and four (I, II, III, IV) in Brazil. The time of most recent common ancestor (tMRCA) of all strains was many centuries ago, but the lineages detected in South America (II and V) had tMRCA in recent decades. IncFIC(FII), IncFII(S) and ColRNAI were plasmid replicons frequently found in the lineages from Brazil, but antimicrobial resistance genes were scarce. Only two resistance genes (<i>aac(6’)-Iaa</i> and <i>mdf(A)</i>) were detected in most strains, while other two (<i>blaTEM-106</i> and <i>fosA3</i>) were present in some isolates. It was also observed important differences in the virulence genomic profile of the different lineages, highlighting lineage IV, which does not carry the very important <i>Salmonella</i> pathogenicity island 1 (SPI1) genes cluster. In summary, this study reveals the emergence and dissemination of four different lineages of <i>S.</i> Gallinarum in Brazil.