Phenotypic and genotypic characterization of Salmonella spp. isolates in Portugal

Abstract

Salmonellosis remains one of the most common causes of gastrointestinal infection in the world, and represents a considerable burden in developing and developed countries. As such, Salmonella surveillance is essential to control infection and decrease the economic burden of the disease, and the Portuguese National Institute of Health has been working in this field roughly since 1950. Considering the importance of the surveillance of Salmonella enterica, the main goal of this work was to contribute to a better knowledge of relevant serovars circulating in Portugal, either the most common, or serovars exhibiting important fitness traits that confer ecological advantages over other strains. In order to achieve this objective, first we analysed decades of data and established the trends of Salmonella enterica serovars circulating in Portugal. Additionally, whole-genome sequencing (WGS) was implemented at the National Reference Laboratory to the surveillance of Salmonella enterica, and was evaluated as a substitute of traditional typing methods, such as serotyping and multiple-locus variable number tandem repeat analysis. WGS proved to be a highly discriminatory method for the detection of suspected outbreaks and even previously undetected clusters. We identified several isolates carrying multiple resistance markers and mobile genetic elements that confer the potential of persistence and spread of these bacteria. This PhD dissertation highlights the need for the adjustment of the existing regulations for foodstuffs monitoring and the investigation of safe control measures in animal production, as a means to control the spread of resistant and persistent clones that may contribute to the increase of severe infections and to the spread of those markers to other bacteria. This work stands as an important contribution for the insight on Salmonella enterica isolates circulating in Portugal, as well as a contribution for the reinforcement of the capacitation of the Portuguese National Reference Laboratory.