Development of new molecular tools for characterizing Salmonella spp. strains isolated in Belgium, with new insights into monophasic variants of serovar Typhimurium

The epidemiological follow-up of food-borne pathogens, including Salmonella spp., is important to facilitate tracking of contamination sources and thereby limit infections and improve security of the food chain. Molecular subtyping methods are key tools for this surveillance approach. A new multiplex molecular assay was developed to support the surveillance of the most frequently encountered Salmonella enterica serovars circulating in the food chain and infecting humans in Belgium or posing a threat to animal health, namely Typhimurium, Salmonella Typhimurium monophasic variants (STMV), Enteritidis, Kentucky, Derby, Infantis, Newport, Paratyphi B, Brandenburg, Virchow, Hadar, Ohio, Choleraesuis and Gallinarum. This method consists in a 41-plex Ligase Chain Reaction (LCR) assay targeting polymorphic sites of the Salmonella genome, followed by detection on a bead-array platform. This single-well assay is particularly appropriate to answer the following diagnostic queries: (i) characterize isolates belonging to the following serovars: Typhimurium, STMV, Paratyphi B, Gallinarum, Virchow, Brandenburg and Hadar, (ii) identify the monophasic variants of Salmonella Typhimurium and classify them into STMV lineages, (iii) identify Salmonella Gallinarum and Paratyphi B at biovar or variant level, respectively, (iv) discriminate putative lineages of the polyphyletic Kentucky serovar, and (v) guide the serovar diagnostic of an isolate among the most encountered serovars and identify the Typhimurium serovar. This assay can replace several existing PCR assays, in particular for the identification of the different monophasic variants of Salmonella Typhimurium. This multiplex approach is easy to perform and requires limited handwork. It can be applied to answer other diagnostic questions on Salmonella spp. and on other pathogens. A molecular assessment of the STMV isolates circulating in the Belgian food chain showed that different subtypes were associated to human infections with several putative contamination sources. The pig and pork sector represented a major source of STMV isolated in Belgium. New genotypes were discovered and explained the monophasic character of atypical variants. PCR and LCR tools, as well as a recommended laboratory scenario, are provided to identify and to follow-up the main genotypes observed. These findings will assist the routine diagnosis of the STMV isolates.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 201