Salmonella sp. em águas superficiais de regiões agropecuárias do Estado do Rio de Janeiro: ocorrência, identidade, virulência e resistência a antimicrobianos

Abstract

Salmonella sp. is a bacterial genus of the Enterobacteriaceae family, composed of two species: S. bongori and S. enterica, the latter being of greater clinical and economic relevance due to its subspecies S. enterica subsp. enterica (I), which is responsible for causing infections in warm-blooded animals such as humans, cattle, and poultry. This pathogen plays a central role in the context of Waterborne and Foodborne Diseases (WFDs), impacting human, animal, and environmental health. Its association with hosts such as cattle and broiler chickens makes agricultural production regions potential epicenters of dissemination, either through water sources or food products. In this context, the aim of this study was to investigate the occurrence of Salmonella in water bodies in agricultural regions of the State of Rio de Janeiro, focusing on area impacted by cattle farming, broiler chicken production, and horticulture, as well as to characterize aspects of the isolates, such as serovars, virulome, resistome, and plasmidome. A total of 313 water samples were collected from rivers, streams, and creeks within the hydrographic basins of Médio Paraíba do Sul (MPS; marked by cattle farming and horticulture) and Piabanha (Pb; with intense horticulture and broiler chicken farming). From 181 (58%) of these samples, Salmonella was successfully isolated. After isolation, screening by RAPD, sequencing of up to five isolates per water sample, and bioinformatics analyses, 308 isolates were selected as representatives of the collection (all those that were determined to be non-clonal within each evaluated water sample). Among them, 46 serovars were identified, with emphasis on Panama (44/308), Newport (43/308), Typhimurium (27/308), and Saphra (23/308), with the first three serovars present in both basins and the last one exclusive to MPS. A total of 146 virulence genes were detected, including operons such as spv, pef, rck, and yopJ/yopP, which were associated with plasmids of the incompatibility group IncF, commonly linked to invasive virulence genes. Additionally, resistance mechanisms to β-lactams, aminoglycosides, tetracyclines, phenicols, quinolones, sulfonamide-trimethoprim were identified in chromosomal genes (mutations in gyrA and ramR) and in contigs associated with plasmid markers such as Col440I (containing qnrB19), ColRNAI (aph(3'')-Ib, aph(6)-Id, sul2, and tet(A)), IncC/A2 (sul2 and tet(A)), IncFIC (floR and tet(A)), IncR, and IncX (blaTEM-1, blaTEM-135, and tet(A)), as well as genes blaCMY-2, aadA1, aadA2, tet(B), tet(C), qnrS1, and dfrA in plasmids without a defined Inc group. The fosA7 gene (fosfomycin) was found in the genome of all Saphra isolates. The results of this study provide unique insights into the phylogeny, virulence, resistance, and plasmidome of Salmonella in water bodies of agricultural regions in Rio de Janeiro, contributing to a better understanding of the dissemination and adaptation of this pathogen in this region.