Genomic and Evolutionary Analysis of Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa.

Since its emergence in the beginning of the 90's, multidrug-resistant (MDR) subsp serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Kentucky ST198 genomes (n=229). All the 19 sequenced Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the , , -, , , and (A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and A and C mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1-4, SPI 9 or C63PI) was identified among the 229 public Kentucky genomes. The phylogenetic analysis revealed that almost all Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.