Antibiotic resistance and first comprehensive genomic characteristics of <i>Salmonella</i> Gallinarum isolated from poultry in Morocco

Fowl typhoid, caused by Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SG), is a critical disease listed by the World Organization for Animal Health (WOAH) that causes substantial economic losses in the global poultry industry. In this study, 23 SG strains were isolated from poultry in Morocco showing typical lesions of fowl typhoid, including splenomegaly and hepatomegaly with necrotic foci and peritonitis. The isolates were biochemically identified and tested for phenotypic antibiotic susceptibility. Whole genome sequencing (WGS) was used for studying the genetic characteristics of isolated strains and to determine the virulence and antibiotic-resistance markers. Antibiotic susceptibility testing revealed that 13 (56.5%) isolates were resistant to flumequine with eight (34.8%) and 9 (39.1%) isolates having intermediate resistance to tetracycline and colistin, respectively. WGS revealed 26 resistance genes, coding mainly for efflux pumps and beta-lactamase, including aac(6’)-Iaa, aac(3)-IIa and blaTEM-1a. Virulence profiling identified 107 genes and multiple Salmonella pathogenicity islands (SPIs), while mobile genetic elements analysis detected the IncI1-(α) plasmid in two strains, previously unreported in avian SG. Phylogenomic analysis showed that the isolated strains in this study were closely related to SG strains in the NCBI database, with eight strains phylogenetically linked to the SG9R vaccinal strain. Single Nucleotide Polymorphism (SNP) analysis, using the parental SG9 vaccine strain as a reference, revealed a low number of variants in these eight strains, suggesting reversion to virulence. These findings enhance understanding of SG’s genomic features, aiding improved management of fowl typhoid, vaccine programme development and reduction of antibiotic resistance in poultry. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in Salmonella Gallinarum. Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2. SNP analysis suggested reversion to virulence in eight vaccine-related strains. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in Salmonella Gallinarum. Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2. SNP analysis suggested reversion to virulence in eight vaccine-related strains.