Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates.

Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported clade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (blaTEM-70, blaTEM-148 and blaTEM-198) than the gene blaCTX-M-65 found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates. The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.

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, aphA1-Iab, blaTEM-1, blaPSE-1, tetA) was highly correlated with phenotypic profiles of aminoglycoside, ß-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.

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. MLST resulted in 4 sequence types (STs) for each serotype, including one novel ST for serotype Mikawasima. Similarly, PFGE revealed four different XbaI PFGE patterns. The results of this survey, obtained by the most common subtyping methods (i.e. serotyping, MLST 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.