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    Analysis of Virulence Factors and Antimicrobial Resistance in Salmonella Using Molecular Techniques and Identification of Clonal Relationships Among the Strains
    (Mary Ann Liebert, Inc, 2018) Unlu, Ozge; Aktas, Zerrin; Tugrul, Hamdi Murat
    A total of 50 Salmonella enterica strains were isolated from clinical samples from 2009 to 2012 and analyzed for the presence of virulence genes found in SPI-1, SPI-2, and plasmids. The distribution and frequency of the antimicrobial resistance genes and plasmids were revealed, and pulsed-field gel electrophoresis (PFGE) patterns were investigated. Five genes were identified from the seven strains with resistance or intermediate resistance to ampicillin: blaSHV-1 (present in six strains), qnrS1 (present in five strains), blaTEM-1 (present in three strains), blaCTX-M-1 (present in one strain), and qnrB1 (present in one strain). One trimethoprim-sulfamethoxazole-resistant strain was positive for sulI but negative for sulII. In addition, we detected TEM-1 and qnrS1 in one strain; SHV-1 and qnrS1 in two strains; TEM-1, SHV-1, CTX-M-1, and qnrS1 in one strain; TEM-1, SHV-1, and qnrB1 in one strain; and SHV-1 and sulI genes in one strain together. Plasmid-based replicon typing assay revealed that all 50 strains carried FIIS, 13 carried I1, 1 carried I2, 4 carried P, 1 carried A/C, and 4 carried X1 replicon. PFGE was used to type 46 of the 50 strains and classify them into 22 major groups, 33 pulsotypes, and 8 major clusters. All strains carried all the virulence genes of interest on both Salmonella Pathogenicity Islands 1 and 2 and plasmids suggested high potential for pathogenicity. All antimicrobial-resistant strains contained at least one of the resistance genes of interest, confirming a phenotype-genotype association in antimicrobial resistance.
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    Comparison of microbial adhesion and biofilm formation on orthodontic wax materials; an in vitro study
    (Elsevier Taiwan, 2020) Bozkurt, Aylin Pasaoglu; Unlu, Ozge; Demirci, Mehmet
    Background/purpose: Orthodontic wax materials are available on the dental market and are given by orthodontists due to pain, sores and irritation caused by treatment. The aim of the study was to compare biofilm formation and microbial adhesion at different time points on different protective materials used against orthodontic wounds in vitro. Materials and methods: Microbial adhesion and biofilm formation were evaluated against Streptococcus mutans ATCC 25175 and Lactobacillus acidophilus ATCC 4356 standard strains on orthodontic wax materials at the 0, 24th, 48th, 72nd, 96th and 120th hour. The Kruskal Wallis test and Bonferroni test were used for statistical evaluations. Statistical significance was set at p < 0.05. Results: It was observed that S. mutans formed statistically significantly more biofilm on OrthoDots (R) CLEAR (OrVance) than Ora-Aid (TBM Corporation) at the 48th hour (p < 0.05). Furthermore, L. acidophilus formed statistically significantly more biofilm on OrthoDots (R) CLEAR (OrVance) than Brace Gard (R)(Infa-Lab Inc.) at the 72nd, 96th and 120th hours (p < 0.05). Conclusion: Significant differences were noted among the different orthodontic wax materials and both S. mutans and L. acidophilus created biofilm on all waxes at different time points in vitro. To prevent biofilm formation, these waxes need to be refreshed and should not be used for more than 24 h. According to our study, biofilm production performances of pathogens on Brace Gard (R)(Infa-Lab Inc.) are minimal and therefore it may be a better option to use in clinics. However, to our knowledge, this is the first study investigating biofilm formation on waxes and more studies are needed in this field. (c) 2020 Association for Dental Sciences of the Republic of China. Publishing services by Elsevier B.V.
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    Could Long Non-Coding RNA MEG3 and PTENP1 Interact with miR-21 in the Pathogenesis of Non-Alcoholic Fatty Liver Disease?
    (Mdpi, 2023) Erdem, Mustafa Genco; Unlu, Ozge; Demirci, Mehmet
    NAFLD is the most common cause of chronic liver disease worldwide. The miRNAs and lncRNAs are important endogenous ncRNAs families that can regulate molecular mechanisms. The aim of this study was to analyze the miRNA and lncRNA expression profiles in serum samples of NAFLD patients with different types of hepatosteatosis compared to healthy controls by the qPCR method. A total of180 NAFLD patients and 60 healthy controls were included. miRCURY LNA miRNA miRNome PCR human panel I + II kit and LncProfiler qPCR Array Kit were used to detect miRNA and lncRNA expression, respectively. DIANA miRPath and DIANA-lncBase web servers were used for interaction analysis. As a result, 75 miRNA and 24 lncRNA expression changes were determined. For miRNAs and lncRNAs, 30 and 5 were downregulated and 45 and 19 were upregulated, respectively. hsa-miR-21 was upregulated 2-fold whereas miR-197 was downregulated 0.25-fold. Among lncRNAs, NEAT1 was upregulated 2.9-fold while lncRNA MEG3 was downregulated 0.41-fold. A weak correlation was found between hsa-miR-122 and lncRNA MALAT1. As a conclusion, it is clear that lncRNA-miRNA interaction is involved in the molecular mechanisms of the emergence of NAFLD. The lncRNAs MEG3 and PTENP1 interacted with hsa-miR-21. It was thought that this interaction should be investigated as a biomarker for the development of NAFLD.
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    Could Prior COVID-19 Affect the Neutralizing Antibody after the Third BNT162b2 Booster Dose: A Longitudinal Study
    (Mdpi, 2023) Erdem, Mustafa Genco; Unlu, Ozge; Buber, Suleyman; Demirci, Mehmet; Kocazeybek, Bekir Sami
    Vaccination is an essential public health measure for preventing the spread of illness during this continuing COVID-19 epidemic. The immune response developed by the host or the continuation of the immunological response caused by vaccination is crucial since it might alter the epidemic's prognosis. In our study, we aimed to determine the titers of anti-S-RBD antibody and surrogate neutralizing antibody (snAb) formed before and after the third dose of the BNT162b2 vaccination (on the 15th, 60th, and 90th days) in healthy adults who did not have any comorbidity either with or without prior SARS-CoV-2 infection. In this longitudinal prospective study, 300 healthy persons were randomly included between January and February 2022, following two doses of BNT162b2 immunization and before a third dosage. Blood was drawn from the peripheral veins. SARS-CoV-2 NCP IgG and anti-S-RBD IgG levels were detected by the CMIA method, and a surrogate neutralizing antibody was seen by the ELISA method. Our study included 154 (51.3%) female and 146 (48.7%) male (total 300) participants. The participants' median age was 32.5 (IQR:24-38). It was discovered that 208 individuals (69.3%) had never been infected with SARS-CoV-2, whereas 92 participants (30.7%) had SARS-CoV-2 infections in the past. Anti-S-RBD IgG and nAb IH% levels increased 5.94- and 1.26-fold on day 15, 3.63- and 1.22-fold on day 60, and 2.33- and 1.26-fold on day 90 after the third BNT162b2 vaccine dosage compared to pre-vaccination values (Day 0). In addition, the decrease in anti-S-RBD IgG levels on the 60th and 90th days was significantly different in the group without prior SARS-CoV-2 infection compared to the group with past SARS-CoV-2 infection (p < 0.05). In conclusion, it was observed that prior SARS-CoV-2 infection and the third BNT162b2 vaccine dose led to a lower decrease in both nAb and anti-S-RBD IgG levels. To evaluate the vaccine's effectiveness and update immunization programs, however, it is necessary to perform multicenter, longer-term, and comprehensive investigations on healthy individuals without immune response issues, as there are still circulating variants.
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    Detection of HEV RNA genotypes in amounts and Raw Milks Obtained from Different Animals
    (Ankara Microbiology Soc, 2019) Demirci, Mehmet; Yigin, Akin; Unlu, Ozge; Kilic Altun, Serap
    Hepatitis E virus (HEV) is one of the major foodborne viral pathogens transmitted through the fecal-oral route. Four genotypes of HEV are known to infect humans and it is reported that different types of HEV are active in zoonotic transitions. It is known that the HEV genotype 1 and HEV genotype 2 infections are generally acute and the HEV genotype 3 infections are chronic. Therefore, in the studies related to HEV infections, it is important to determine the genotypes to monitortreatment regimens. Although raw milk is often used in communities due to its low cost, there are limited data on the rates and the genotypes of HEV in our country and in the world. In light of this information, we aimed to investigate epidemiologically the quantity and genotypes of HEV RNA in 231 raw milk (48 cow milk, 65 goat milk, 65 sheep milk, and 53 donkey milk) samples. Viral RNAs were isolated from raw milk samples and the ORF2 region of HEV was investigated by the qRt-PCR method to determine quantitatively the presence of HEV RNA. In addition, among HEV RNA positive samples, the ORF2 region of HEV was amplified by nested PCR and the amplicons were sequenced. HEV RNA was detected in 47 (20.34%) raw milk samples, Positivity was detected in 14 (29.16%) of cow milk, 12 (18.46%) of goat milk, 8 of sheep milk (12.3) and 13 of donkey milk (24.5%). The amount of HEV RNA in cow milk found as the highest in both proportion and quantity. When the distribution of the HEV genotypes in the 47 positive samples was examined, 27 (57.44%) HEV genotype 1a, 10 (21.27%) HEV genotype 1 b, 4 (8.5%) HEV genotype 4c, 2 (4.2%) HEV genotype 3a, (2.13) HEV genotype lc, 1 (2.13%) HEV genotype 3e, 1 (2.13%) HEV genotype 3f and 1 (2.13%) HEV genotype 3g were determined. Although genotype la is more frequent, it has been revealed that different genotypes encountered in our country. In conclusion, it has been determined that HEV, one of the major foodborne viral agents, may be encountered in raw milk, and the genotypes that can cause infections in human are found especially in raw milk from animal sources. For the prevention of foodborne outbreaks, the presence of HEV in raw milk should not be ignored.
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    A Longitudinal Study in Turkiye of Host Ability to Produce Antibodies following a Third Homologous BNT162b2 Vaccination
    (Mdpi, 2023) Erdem, Mustafa Genco; Unlu, Ozge; Demirci, Mehmet
    Obesity is a multifaceted, complex condition that has negative impacts on one's health. There are conflicting reports regarding the COVID-19 vaccine's ability to induce antibody formation in obese people. Our study aimed to determine anti-S-RBD IgG and surrogate neutralizing antibody (snAb) levels before and after the third Pfizer-BioNTech (BNT162b2) vaccination (at 15, 60, 90, and 120 days) in normal-weight adults, overweight, and obese individuals without any comorbidity or previous SARS-CoV-2 infection history, but it did not evaluate the response to the first two doses. In this longitudinal prospective study in Istanbul, Turkey, a total of 323 consecutive adult individuals (141 normal weight, 108 overweight, and 74 patients with obesity) were included. Peripheral blood samples were collected. Anti-S-RBD IgG and surrogate neutralizing antibody levels were detected using the ELISA method. After the third dose of BNT162b2 vaccination, obese patients had significantly lower levels of snAb against SARS-CoV-2 compared with normal-weight controls, but the levels otherwise did not differ between the study groups. Across all individuals in our cohort, titers peaked about a month after this third vaccination and then gradually faded. Anti-S-RBD IgG and snAb IH% levels against SARS-CoV-2 were not correlated with IL-6 and TNF-alpha levels. In conclusion, anti-S-RBD IgG titers and snAb IH% levels against SARS-CoV-2 were determined longitudinally for 120 days after the third homologous BNT162b2 vaccination. Although there were no significant differences in anti-S-RBD IgG, we found significant differences in the snAb IH% levels against SARS-CoV-2 between obese and healthy control subjects.
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    Oral Microbiota Signatures in the Pathogenesis of Euthyroid Hashimoto's Thyroiditis
    (Mdpi, 2023) Erdem, Mustafa Genco; Unlu, Ozge; Ates, Fatma; Karis, Denizhan; Demirci, Mehmet
    One of the most prevalent autoimmune illnesses in the world is Hashimoto's thyroiditis, whose pathogenesis is still unknown. The gut-thyroid axis is frequently examined, and although oral health affects thyroid functions, there are limited data on how oral microbiota is linked to Hashimoto's thyroiditis. The study aims to identify the oral microbiota from saliva samples taken from treated (with levothyroxine) and untreated female euthyroid Hashimoto's thyroiditis patients as well as healthy controls who were age- and sex-matched to compare the oral microbiota across the groups and to contribute preliminary data to the literature. This study was designed as a single-center cross-sectional observational study. Sixty (60) female patients with euthyroid Hashimoto's thyroiditis (HT) and eighteen (18) age- and gender-matched healthy controls were included in this study. Unstimulated saliva samples were collected. After DNA isolation, sequencing was performed by targeting the V3-V4 gene regions of the 16S rRNA on the MiSeq instrument. R scripts and SPSS were used for bioinformatic and statistical analysis. No significant differences were found in the diversity indices. However, Patescibacteria phylum showed a significantly higher abundance (3.59 vs. 1.12; p = 0.022) in the oral microbiota of HT patients compared to HC. In the oral microbiota, the euthyroid HT group had approximately 7, 9, and 10-fold higher levels of the Gemella, Enterococcus, and Bacillus genera levels than healthy controls, respectively. In conclusion, the results of our study demonstrated that Hashimoto's thyroiditis causes changes in the oral microbiota, whereas the medicine used to treat the condition had no such effects. Therefore, revealing the core oral microbiota and long-term follow-up of the HT process by conducting extensive and multicenter studies might provide some important data for understanding the pathogenesis of the disease.