LAUSR

ABSTRACT Salmonella enterica 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 S. Gallinarum lineages from Brazil. Twelve whole-genome sequences (WGS) of different S. Gallinarum strains isolated from Brazilian poultry farms (2014–2018) were obtained and used to construct a dataset with 31 other previously published sequences (five more from Brazil). The phylogenetic diversity, temporal evolution and antimicrobial resistance/virulence genomic profile of Brazilian strains were evaluated. Sixteen (94.1%) Brazilian strains were from sequence type ST78 and one (5.9%) was from ST331. All S. 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 two lineages detected only 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 (aac(6’)-Iaa and mdf(A)) were detected in most strains, while two other (blaTEM-106 and fosA3) were present in some isolates. Important differences were also observed in the virulence genomic profile of the different lineages, highlighting lineage IV, which does not carry the very important Salmonella pathogenicity island 1 (SPI1) gene cluster. In summary, this study reveals the emergence and dissemination of four different lineages of S. Gallinarum in Brazil. RESEARCH HIGHLIGHTS Fowl typhoid (FT) is a concerning poultry disease caused by S. Gallinarum. Five S. Gallinarum lineages (I to V) were demonstrated in South American farms. S. Gallinarum lineages have specific antimicrobial resistance / virulence genomic profiles. Main FT outbreaks in Brazil have been caused by the specific lineage II.