Molecular characterization of salmonella isolates from animals and various foods /

Durul, Bora
Salmonella, which is a Gram-negative human and animal pathogen, poses a significant threat to public health with its existence and survival in the farm to fork chain. Of the greater importance, Salmonella enterica subsp. enterica, which covers 60 % of nearly 2500 Salmonella serotypes, causes diseases in mammals with varying host affiliations and pathogenity levels. In order that consumer safety can be assured, elimination of this harmful pathogen from the farm to fork chain is a must, thereby bringing the importance of the comprehensive investigations of the diversity of Salmonella pathogen. The objective of this research is to use genotypic and phenotypic methods to have a better understanding on the Salmonella diversity by analyzing samples from animals and various foods. Thus, for this aim, firstly, samples were collected from street food and also animal clinical cases. The final goal was to gain 50 food Salmonella isolates and 50 Salmonella animal isolates, at least, during four seasons of a year in the pilot region, Şanlıurfa. Presence of Salmonella suspected colonies was investigated through conventional methods. Then, suspected colonies were confirmed as Salmonella by using polymerase chain reaction (PCR) of Salmonella specific gene, invA. Following this, confirmed colonies were analyzed by phenotypic and genotypic methods. For the phenotypic analysis, a classical method, serotyping, was used. Moreover, for the genotypic analysis part, multi locus sequence typing (MLST), one of the most preferred genotype-based methods, providing both a high discriminatory power among subtypes and an extensive phylogenetic analysis, was utilized according to seven gene MLST (aroC, dnaN, hemD, hisD, purE, sucA and thrA) scheme designed by University College Cork. Then, phylogenetic trees of the collected isolates were constructed by using bioinformatics software. As a result of the study, 59 food-origin and 53 animal-origin isolates were recovered from 192 food samples and 355 animal fecal samples, which mean that 30.1 % of food samples and 14.9 % animal samples were Salmonella-positive. Furthermore, while MLST and serotyping had congruent discriminatory power in food isolates, MLST provided intra-serotype discrimination within several serotypes in animal isolates. On the other hand, results of both subtyping methods indicate a possible affiliation between several subtypes and their source. Moreover, in addition to 4 previously unidentified sequence types that were discovered by MLST in this study, subtype Telaviv (ST 1068) is noteworthy owing to its high prevalence in food and animal samples in this study and its large absence in the scientific literature and other surveillance studies. In conclusion, combining the power of genotype-based MLST and phenotype-based serotyping, this study provided us a clue about the unique Salmonella diversity in the pilot region. In addition to being a pioneer surveillance study in Turkey where genotypic and phenotypic approaches are utilized together, results of this study are useful in the maintenance of a new publicly available pathogen database as well as in further outbreak investigations.