Abstract

Salmonella enterica remains a major foodborne pathogen globally but little attention has been paid to infrequent serovars in environmental settings. We report the occurrence of 30 rare S. enterica serovars isolated from environmental water sources between 2021 and 2022 in semiarid northeastern Brazil. We conducted two risk-based field campaigns at shoreline access points in 10 reservoirs associated with the three largest river basins in the state. Salmonella enterica was recovered from 175 out of 230 water samples, yielding 2903 isolates. Of these, 938 were selected for whole-genome sequencing (WGS). Genome assembly and downstream analyses identified 65 unique serovars, including 68 isolates belonging to 30 rare serovars. Salmonella Carrau (n = 14), S. Oran (n = 9), S. Gaminara (n = 5), and S. Urbana (n = 4) were the most frequent rare serovars. WGS analysis revealed the presence of antimicrobial resistance genes (ARGs) in all isolates. The highest abundances were associated with ARGs conferrying resistance to aminoglycosides [aac(6 ')-Iaa (100%)], quinolones (parC:p.T57S [98.1%] and qnrB19 [3.77%]), and fosfomycin (fosA7 [3.77%]). Some isolates carried plasmids (IncX3, IncFII [S], IncFII [Cf], Col [pHAD28], and IncFII [SARC14]) that could facilitate the spread of antimicrobial resistance. Phylogenetic analysis indicated the presence of distinct clades for each serovar. Interestingly, 20 serovars are endemic lineages circulating in Brazil, except S. Kiambu, which belongs to an international lineage. These findings underscore the importance of environmental monitoring and understanding the distribution of Salmonella in water sources to safeguard public health and prevent the spread of antimicrobial resistance.