Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000–2016

Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S . enterica serovars S . Schwarzengrund ST96, S . Typhimurium ST19, S . Minnesota ST548, S . Infantis ST32, S . Heidelberg ST15, S . Newport ST45, S . Brandenburg ST65 and S . Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S . Typhimurium from food chain), qnrB19, qnrS1 , bla CTX-M-8 , bla CTX-M-2 and bla CMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S . enterica serovars S . Infantis, S . Schwarzengrund, S . Minnesota, S . Kentucky and S . Brandenburg. In brief, ocurrence and persistence of international lineages of S . enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.