Exploring the genomic and antimicrobial resistance tapestry: comparative insights into <i>Salmonella enterica</i> serotypes Agona, Braenderup, Muenchen, and Panama in Latin American surface waters

Surface waters function as ecological niches where <i>Salmonella enterica</i> can persist and disseminate to fresh produce production systems. We examined the genomic characteristics of <i>S. enterica</i> serotypes Agona (<i>n</i> = 86), Braenderup (<i>n</i> = 47), Muenchen (<i>n</i> = 53), and Panama (<i>n</i> = 69) isolates from surface waters in Chile, Mexico, and Brazil between 2019 and 2022. Mexican isolates consistently displayed a higher occurrence of genotypic antimicrobial resistance (AMR) than Chilean and Brazilian isolates. All <i>S</i>. Agona isolates exhibited the presence of <i>fosA7.2</i>, while <i>qnrB19</i> emerged as the predominant AMR gene (ARG) among <i>S</i>. Braenderup isolates. <i>S</i>. Muenchen isolates from Chile displayed an absence of any ARGs, while those from Mexico and Brazil predominantly carried <i>qnrB19</i>. Among <i>S</i>. Panama isolates from Chile, <i>aadA1</i>, <i>floR</i>, <i>sat2</i>, and <i>tet(B</i>) were the most prevalent ARGs, whereas those from Mexico and Brazil harbored <i>tet(A</i>), and <i>floR</i> and <i>tet(A</i>) as the leading ARGs, respectively. ARG sharing among isolates and ARG co-occurrence within individual isolates were prevalent across countries and serotypes. All isolates containing integrons exhibited genotypic multidrug resistance. The principal coordinates analysis reveals distinct clustering patterns based on country, serotype, number of ARGs per isolate, and plasmid and integron presence/absence. The whole-genome phylogenetic analysis demonstrates clear clusters, each associated with their respective countries. However, a notable exception was observed with one <i>S</i>. Agona isolate from Brazil closely related to two isolates from Chile, differing by only 18 and 19 single-nucleotide polymorphisms, respectively.IMPORTANCEThis comprehensive study explored the intricate genomic landscapes of <i>S</i>. Agona, Braenderup, Muenchen, and Panama isolates from surface waters across Chile, Mexico, and Brazil. By filling important knowledge gaps related to the genomic characteristics of these serotypes, the research offers a nuanced understanding of these serotypes as potential reservoirs for multidrug resistance. Our findings emphasize the urgency of targeted interventions to mitigate the emergence and dissemination of multidrug-resistant <i>Salmonella enterica</i>. This work underscores the need for informed policies and collaborative efforts to address the risks posed by <i>S. enterica</i> in Latin American surface waters.