# Surface water as a source of rare Salmonella enterica serovars in semiarid northeastern Brazil

## TL;DR

Scientists found rare Salmonella types in water from dry regions of Brazil, some of which resist antibiotics and could spread drug resistance.

## Contribution

Identification of 30 rare Salmonella serovars in environmental waters and their antimicrobial resistance profiles in a semiarid region.

## Key findings

- 30 rare Salmonella serovars were identified in water samples from northeastern Brazil.
- Most isolates showed resistance to gentamicin and carried multidrug efflux pump genes.
- Phylogenetic analysis revealed local lineages distinct from international strains.

## 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.

Rare Salmonella enterica serovars were recovered from surface waters in semiarid northeastern Brazil.Most isolates showed resistance to gentamicin and harbored multidrug efflux pump genes (mdsA/B).Whole‐genome sequencing revealed 22 sequence types, most reported for the first time in Brazil.Phylogenetic analysis showed local Salmonella lineages unrelated to international strains.Rare serovars pose overlooked risks to agrifood chains and public health in low‐income rural areas.

Rare Salmonella enterica serovars were recovered from surface waters in semiarid northeastern Brazil.

Most isolates showed resistance to gentamicin and harbored multidrug efflux pump genes (mdsA/B).

Whole‐genome sequencing revealed 22 sequence types, most reported for the first time in Brazil.

Phylogenetic analysis showed local Salmonella lineages unrelated to international strains.

Rare serovars pose overlooked risks to agrifood chains and public health in low‐income rural areas.

Salmonella is a dangerous germ that makes people sick when they eat contaminated food, but scientists do not pay much attention to rare types of this germ, which might still be harmful to people's health. We looked for Salmonella germs in water from lakes and rivers in northeastern Brazil, a very dry region, by collecting water samples from 10 large dams between 2021 and 2022. We discovered 30 different rare types of Salmonella in the water samples, with the most common rare types being Carrau, Oran, Gaminara, and Urbana, which was surprising because these types are not usually found in water. When we studied these germs more closely using advanced technology, we found that some of these Salmonella germs can resist medicines (antibiotics) that doctors use to treat infections, which means if someone gets sick from these germs, it might be harder to cure them. Moreover, they can transfer this resistance to other germs. Our research shows that even rare types of Salmonella in water sources.