Gıda ve hayvanlardaki salmonella izolat çeşitliliğinin moleküler düzeyde belirlenmesi.

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.M.S. - Master of Scienc

GIDALARDAKİ VE KLİNİK HAYVAN VAKALARINDAKİ SALMONELLA İZOLAT ÇEŞİTLİLİĞİNİN MOLEKÜLER DÜZEYDE BELİRLENMESİ

GIDALARDAKİ VE KLİNİK HAYVAN VAKALARINDAKİ SALMONELLA İZOLAT ÇEŞİTLİLİĞİNİN MOLEKÜLER DÜZEYDE BELİRLENMES

Subtyping of Salmonella Food Isolates Suggests the Geographic Clustering of Serotype Telaviv

Salmonella is commonly found in a variety of food products and is a major cause of bacterial foodborne illness throughout the world. In this study, we investigated the prevalence and diversity of Salmonella in eight different food types: sheep ground meat, cow ground meat, chicken meat, cow offal, traditional Sanliurfa cheese, unripened feta cheese, pistachios, and isot (a spice blend of dried red peppers specific to Sanliurfa), traditionally and commonly consumed in Turkey. Among 192 food samples, Salmonella was detected in 59 samples, with the highest prevalence in raw poultry parts (58%) and offal (58%) samples, while Salmonella was not detected in pistachios and dried red pepper. Resultant Salmonella isolates were characterized by serotyping, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Ten different serotypes represented 10 MLST sequence types (STs) with 1 novel ST and 17 PFGE types. Antimicrobial resistance profiling revealed that 30.5% of the isolates were resistant to two or more antimicrobials. Salmonella enterica subsp. enterica serotype Telaviv, which is rare throughout the world, was the second most common serotype isolated from food samples in this study, suggesting that this serotype might be one of the subtypes that is endemic to Turkey

Salmonella surveillance on fresh produce in retail in Turkey

Although Turkey is one of the major producers of fruits and vegetables in the world, there has been no information available on the prevalence of pathogens in fresh produce. To fill this gap, we collected 503 fresh produce samples including tomato, parsley, iceberg lettuce, green-leaf lettuce and five different fresh pepper varieties (i.e., green, kapya, bell, mazamort and Charleston) from 3 major districts within 9 supermarkets and 3 bazaars in Ankara, Turkey to investigate the presence of Salmonella. Salmonella was detected in 0.8% (4/503) of samples by conventional culturing method with molecular confirmation conducted through polymerase chain reaction (PCR). For further characterization of isolates, serotyping, antimicrobial susceptibility testing, multi-locus sequence typing (MLST; aroC, thrA, purE, sucA, hisD, hemD and dnaN) and pulsed-field gel electrophoresis (PFGE) were performed. Salmonella enterica subsp. enterica serotypes Anatum, Charity, Enteritidis and Mikawasima were isolated from two parsley, one pepper and one lettuce samples, respectively. MIST resulted in 4 sequence types (STs) for each serotype, including one novel ST for serotype Mikawasima. Similarly, PFGE revealed four different Xbal PFGE patterns. The results of this survey, obtained by the most common subtyping methods (i.e. serotyping, MIST and PFGE) worldwide, contributes to the development of a national database in Turkey, which is essential for investigating the evolutionary pathways, geographical distribution and genetic diversity of Salmonella strains

Phenotyping and genetic characterization of Salmonella enterica isolates from Turkey revealing arise of different features specific to geography

WOS: 000390071600012PubMed ID: 27768932192 Food samples (commonly consumed 8 food types), 355 animal samples (animal feces of bovine, ovine, goat and chicken) and 50 samples from clinical human cases in Sanliurfa city, Turkey in a year were collected to determine the Salmonella enterica subsp. enterica mosaic in Turkey. 161 Salmonella isolates represented 17 serotypes, 20 sequence types (STs) and 44 PFGE patterns (PTs). 3 serotypes, S. Enteritidis, S. Typhimurium and S. Kentucky, were recovered from three different hosts. The highest discriminatory power was obtained by PFGE (SID = 0.945), followed by MLST (SID = 0.902) and serotyping (SID = 0.885) for all isolates. The prevalence of antimicrobial resistance genes (aadA1, aadA2, strA, strB, aphA(1-lab) bla(TEM-1), bla(PSE-1), tetA) was highly correlated with phenotypic profiles of aminoglycoside, beta-lactam and tetracycline groups (kappa >0.85). From our knowledge, this is the first study reporting spatial and temporal distribution of Salmonella species through phenotypic and genetic approaches over farm to fork chain in Turkey. Thus, our data provided further information for evolution, ecology and transmission of Salmonella in Turkey. (C) 2016 Published by Elsevier B.V.Scientific and Technical Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK 3501(1120192)]We acknowledge Dr. Martin Wiedmann from Cornell University for using BioNumerics, Dr. Nihat Dilsiz from Harran University Medicine Faculty, Harran University Veterinary Faculty for the valuable discussion, and Dr. Tolga Can from Middle East Technical University, Computer Engineering for building a web-based database. This work is partially supported by The Scientific and Technical Council of Turkey Grant TUBITAK 3501(1120192)

Phenotyping and genetic characterization of Salmonella enterica isolates from Turkey revealing arise of different features specific to geography

192 Food samples (commonly consumed 8 food types), 355 animal samples (animal feces of bovine, ovine, goat and chicken) and 50 samples from clinical human cases in Sanliurfa city, Turkey in a year were collected to determine the Salmonella enterica subsp. enterica mosaic in Turkey. 161 Salmonella isolates represented 17 serotypes, 20 sequence types (STs) and 44 PFGE patterns (PTs). 3 serotypes, S. Enteritidis, S. Typhimurium and S. Kentucky, were recovered from three different hosts. The highest discriminatory power was obtained by PFGE (SID = 0.945), followed by MLST (SID = 0.902) and serotyping (SID = 0.885) for all isolates. The prevalence of antimicrobial resistance genes (aadA1, aadA2, strA, strB, aphA(1-lab) bla(TEM-1), bla(PSE-1), tetA) was highly correlated with phenotypic profiles of aminoglycoside, beta-lactam and tetracycline groups (kappa >0.85). From our knowledge, this is the first study reporting spatial and temporal distribution of Salmonella species through phenotypic and genetic approaches over farm to fork chain in Turkey. Thus, our data provided further information for evolution, ecology and transmission of Salmonella in Turkey. (C) 2016 Published by Elsevier B.V