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    Antibacterial effects of lidocaine and adrenaline
    (Wiley, 2019) Kesici, Sevgi; Demirci, Mehmet; Kesici, Ugur
    The most commonly used local anaesthetics (LAs) for postoperative analgesia and surgical anaesthesia are lidocaine and bupivacaine. Adrenaline is a vasopressor agent, which is widely used in anaesthesia for many purposes. This study aims to determine the antibacterial efficacy of lidocaine, mupirocin, adrenaline, and lidocaine + adrenaline combination. In our study, the in vitro antimicrobial effect of 1 mL of sterile saline, 20 mg/mL mupirocin, 20 mg/mL lidocaine, 1 mg/mL adrenaline, and 20 mg/mL lidocaine and adrenaline were tested against Staphylococcus aureus American-type culture collection (ATCC) 29213, Pseudomonas aeruginosa ATCC 27853, and Escherichia coli ATCC 25922, classified as Group C (control), Group M (mupirocin), Group L (lidocaine), Group A (adrenaline), and Group LA (lidocaine+adrenaline), respectively. S. aureus ATCC 29213, P. aeruginosa ATCC 27853, and E. coli ATCC 25922 were cultured on Mueller-Hinton agar (Oxoid, UK) plates for 18 to 24 hours at 37 degrees C. Colonies from these plates were suspended in sterile saline, and a 0.5 McFarland turbidity standard suspension (corresponding to 1.5 x 10(8) CFU/mL) of each isolate was prepared. In terms of inhibition zone diameters, S. aureus ATCC 29213 values obtained after 12 and 24 hours of incubation were significantly different between groups (P < .001). According to inhibition zone diameters, Group M > Group LA > Group L > Group C = Group A. P. Aeruginosa ATCC 27853 values obtained after 12 and 24 hours of incubation were significantly different between groups (P < .001). According to inhibition zone diameters, Group M > Group LA > Group L = Group C = Group A. E. coli ATCC 25922 values obtained after 12 and 24 hours of incubation were significantly different between groups (P < .001). According to inhibition zone diameters, Group M > Group LA > Group L > Group C = Group A. It is known that LAs have antimicrobial effect potential in addition to their anaesthetic, analgesic, antiarrhythmic, and anti-inflammatory effects. There are also studies showing the antimicrobial effects of vasopressor agents, which are frequently used, particularly in intensive care unit (ICUs). However, it has been observed in the present study that adrenaline alone did not have any antimicrobial effect. Adrenaline, when used in combination with lidocaine, provides a stronger and broad-spectrum antimicrobial activity, suggesting that its combined use in proper indications will be clinically significant. Because the prevention and treatment of wound infections make a positive contribution to wound healing, the potential of antimicrobial effect of LAs can provide successful results in the prevention and treatment of ICU and wound infections. Thus, an important contribution can be made in terms of reducing the costs of antibacterial treatment and reducing morbidity.
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    Antimicrobial effects of local anaesthetics
    (Wiley, 2019) Kesici, Ugur; Demirci, Mehmet; Kesici, Sevgi
    After the introduction of cocaine to the medical practice, local anaesthetics (LA) became essential in pain control. LA infiltration along the incision may be used to provide surgical anaesthesia or postoperative analgesia. This study aimed to compare the antimicrobial effects of the topical antimicrobial agent mupirocine with those of the LA lidocaine and the combination of lidocaine and adrenalin. In our study, the in vitro antimicrobial effects of 1 mL sterile saline, 20 mg/mL mupirocine, 20 mg/mL Lidocaine, and 20 mg/mL Lidocaine and Adrenaline were tested against Staphylococcus aureus American type culture collection (ATCC) 29213, Pseudomonas aeruginosa ATCC 27853, and Escherichia coli ATCC 25922 as Group C (Control), Group M (Mupirocine), Group L (Lidocaine), and Group LA (Lidocaine + adrenaline), respectively. S aureus ATCC 29213, P aeruginosa ATCC 27853, and E coli ATCC 25922 were cultured onto Mueller-Hinton agar (Oxoid, UK) plates for 18 to 24 hours at 37 degrees C. Colonies from these plates were suspended in sterile saline and a 0.5 McFarland turbidity standard suspension (corresponding to 1.5 x 10(8) CFU/mL) of each isolate was prepared. S Aureus ATCC 29213 inhibition zone diameter values of Group M, Group LA, and Group L were significantly higher compared with the group C (P < 0.05). P aeruginosa ATCC 27853 inhibition zone diameter values of Group M and Group LA were significantly higher compared with the group C (P < 0.05). E coli ATCC 25922 inhibition zone diameter values of Group M, Group LA, and Group L were significantly higher compared to the group C (P < 0.05). LA infiltration along the incision may be used to provide surgical anaesthesia or postoperative analgesia. Considering that LAs show antimicrobial effects besides their analgesic effects, they may contribute to preventing the development and reducing the rate of surgical infections, decreasing the requirement to administer antibiotics. However, caution should be exercised not to antagonise the effective treatment of surgical infections, remembering that controversy on the antimicrobial effects of LAs remains in the literature. Therefore, further comprehensive studies with larger patient populations are warranted to demonstrate the antimicrobial effects of LAs.
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    The Association Between Cagl And Caga, Vacas-M, Baba Genes İn Patients With Gastric Cancer, Duodenal Ulcer, And Non-Ulcer Dyspepsia Related To Helicobacter Pylori
    (Universa Press, Wetteren, Belgium, 2020) Bal, Kadir; Erzin, Yusuf Ziya; Demirci, Mehmet; ;, ve diğerleri
    Introduction: As a component of the cag T4SS, the cagL gene is involved in the translocation of CagA into host cells and is essential for the formation of cag PAI-associated pili between H. pylori and gastric epithelial cells. Aim: We aimed to investigate the clinical association of the cagL gene with other virulence factors (VacA, CagA, EPIYA-C, and BabA protein) of H. pylori strains isolated from GC, duodenal ulcer (DU), and non-ulcer dyspepsia (NUD) cases. Methods: The patient group (PG), including 47 patients (22 GC and 25 DU) and a 25 control group (CG= NUD) were included. Amplification of the H. pylori cagL, cagA, vacA, and babA2 genes and typing of EPIYA motifs were performed by PCR methods. Results: Sixty-one (84.7%) H. pylori strains were detected with cagL (93.6% in SG, 68% in CG). We detected a significant difference between SG and CG for the presence of cagL (p=0.012) but no statistical comparison was done for (?2) EPIYA-C repeats In the comparison of H. pylori strains with cagA/vacAs1m1 and cagA/ vacAs1m2 and babA2 for the presence of cagL, we could not detect a significant difference (p=1). Conclusion: We detected a significant difference between groups for the presence of cagL genotype (p=0.012). The vacAs1m1 (OR: 2.829), genotypes increased the GC and DU risk by 2.8 times, while multiple (?2) EPIYA-C repeats incresed the GC and DU risk by 3.524 times. Gender (to be female) (OR: 0.454) decreased the GC and DU risk by inversly decreased in the multivariate analysis.
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    Association Between Human Leukocyte Antigen Gene Polymorphisms And Multiple Epıya-C Repeats İn Gastrointestinal Disorders
    (Baishideng Publishing Group Inc, 2020) Demirci, Mehmet; Demiryas, Süleyman; Yılmaz, Erkan; Uysal, Ömer; Kepil, Nuray; ., ve diğer.
    Background: Polymorphisms of human leukocyte antigen (HLA) genes are suggested to increase the risk of gastric cancer (GC). Aim: To investigate the HLA allele frequencies of patients with GC relative to a control group in terms of CagA+ multiple (? 2) EPIYA-C repeats. Methods: The patient group comprised 94 patients [44 GC and 50 duodenal ulcer (DU) patients], and the control group comprised 86 individuals [(50 non-ulcer dyspepsia patients and 36 people with asymptomatic Helicobacter pylori (H. pylori)]. Polymerase chain reaction was performed for the amplification of the H. pylori cagA gene and typing of EPIYA motifs. HLA sequence-specific oligonucleotide (SSO) typing was performed using Lifecodes SSO typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1, and HLA-DQA1-B1 kits). Results: The comparison of GC cases in terms of CagA+ multiple (? 2) EPIYA-C repeats showed that only the HLA-DQB1*06 allele [odds ratio (OR): 0.37, P = 0.036] was significantly lower, but significance was lost after correction (Pc = 0.1845). The HLA-DQA1*01 allele had a high ratio in GC cases with multiple EPIYA-C repeats, but this was not significant in the univariate analysis. We compared allele frequencies in the DU cases alone and in GC and DU cases together using the same criterion, and none of the HLA alleles were significantly associated with GC or DU. Also, none of the alleles were detected as independent risk factors after the multivariate analysis. On the other hand, in a multivariate logistic regression with no discriminative criterion, HLA-DQA1*01 (OR = 1.848), HLA-DQB1*06 (OR = 1.821) and HLA-A*02 (OR = 1.579) alleles were detected as independent risk factors for GC and DU. Conclusion: None of the HLA alleles were detected as independent risk factors in terms of CagA+ multiple EPIYA-C repeats. However, HLA-DQA1*01, HLA-DQB1*0601, and HLA-A*2 were independent risk factors with no criterion in the multivariate analysis. We suggest that the association of these alleles with gastric malignancies is not specifically related to cagA and multiple EPIYA C repeats.
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    Association between polymorphisms in HLA-A, HLA-B, HLA-DR, and DQ genes from gastric cancer and duodenal ulcer patients and cagL among cagA-positive Helicobacter pylori strains: The first study in a Turkish population
    (Elsevier, 2020) Kocak, Banu Tufan; Saribas, Suat; Demiryas, Suleyman; Yilmaz, Erkan; Uysal, Omer; Kepil, Nuray; Demirci, Mehmet
    Colonization of the human gastric mucosa by H. pylori may cause peptic and duodenal ulcers (DUs), gastric lymphomas, and gastric cancers. The cagL gene is a component of cag T4SS and is involved in cagA translocation into host. An association between the risk of gastric cancer and the type of HLA class II (DR and/or DQ) was suggested in different populations. The aim of this study was to investigate, the clinical association of the cagL gene with host HLA alleles in H. pylori strains that were isolated from patients with gastric cancer, DU, and non-ulcer dyspepsia (NUD) and to determine the HLA allele that confers susceptibility or resistance for the risk of gastric cancer and DU development in Turkish patients. A total of 94 patients (44 gastric cancer and 50 DU patients; 58 male, 36 female; mean age, 49.6 years), and 86 individuals (50 NUD patients and 36 persons with normal gastrointestinal system [NGIS]; 30 male, 56 female; mean age, 47.3 years) were included as the patient and the control groups, respectively. CagA and cagL were determined by PCR method. DNA from peripheral blood samples was obtained by EZ-DNA extraction kit. For HLA SSO typing, LIFECODES SSO Typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1 and HLA-DQA1/B1 kits) were used. The CagL/CagA positivity distribution in the groups were as follows: 42 (95.4%) gastric cancer, 46 (92%) DU and, 34 (68%) NUD and no NGIS cases. The HLA-DQA1*01 (OR: 3.82) allele was significantly different, suggesting that these individuals with H. pylori strains harbouring the CagL/CagA positivity are susceptible to the risk of gastric cancer and DU, and the HLA-DQA1*05 (OR, 0.318) allele was suggested as a protective allele for the risk of gastric cancer and DU using univariate analyses. HLA-DQA1*01 (OR, 2.21), HLA-DQB1*06 (OR, 2.67), sex (male, OR, 2.27), and CagL/CagA/(< 2) EPIYA C repeats (OR, 5.72) were detected independent risk factors that increased the risk of gastric cancer and DU using multivariate analyses. However, the HLA-DRB1*04 (OR, 0.28) allele was shown to be a protective allele, which decreased the risk of gastric cancer and DU. Gastric pathologies result from an interaction between bacterial virulence factors, host epigenetic and environmental factors, and H. pylori strain heterogeneity, such as genotypic variation among strains and variations in H. pylori populations within an individual host.
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    Bacterial inhibition efficiency of prilocaine and bupivacaine
    (Wiley, 2019) Kesici, Sevgi; Demirci, Mehmet; Kesici, Ugur
    This study aimed to demonstrate the antibacterial effects of bupivacaine and prilocaine on Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. In our study, the in vitro antimicrobial effects of 20 mg/mL prilocaine and 5 mg/mL bupivacaine were tested against a S. aureus American-type culture collection (ATCC) 29213, P. aeruginosa ATCC 27853, and E. coli ATCC 25922, divided into Group P (Prilocaine) and Group B (Bupivacaine), respectively. S. aureus ATCC 29213, P. aeruginosa ATCC 27853, and E. coli ATCC 25922 were cultured on Mueller Hinton agar (Oxoid, Basingstoke, UK) plates for 18 to 24 hours at 37 degrees C. In terms of inhibition zone diameters, inhibition of S. aureus ATCC 29213 was observed in both groups at the 12th and 24th hours. The 12th- and 24th-hour S. aureus ATCC 29213 value was significantly higher in Group P compared with Group B (P = .008). At the 12th and 24th hours, inhibition of E. coli ATCC 25922 was observed in both groups. The 12th- and 24th-hour E. coli ATCC 25922 value was significantly higher in Group P compared with Group B (P = .008). In our study, it was seen that prilocaine and bupivacaine had an antimicrobial effect on S. aureus and E. coli. In the comparison between these two local anesthetics (LAs), this effect was found to be significantly higher in prilocaine than bupivacaine. Therefore, we are of the opinion that antimicrobial effect potentials should also be taken into account in the selection of an LA agent in order to prevent the complications of an infection that might develop during LA infiltration and might lead to serious morbidity.
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    Bacteroidetes and Firmicutes levels in gut microbiota and effects of hosts TLR2/TLR4 gene expression levels in adult type 1 diabetes patients in Istanbul, Turkey
    (Elsevier Science Inc, 2020) Demirci, Mehmet; Tokman, Hrisi Bahar; Taner, Zeynep; Keskin, Fatma Ela; Cagatay, Penbe; Bakar, Yesim Ozturk; Ozyazar, Mucahit
    Aim: The aim of this study was to determine and compare the levels of both Bacteroidetes and Firmicutes in the gut microbiota and TLR2/TLR4 gene expression in the blood of patients with type 1 diabetes mellitus (T1DM) and healthy individuals. These results may serve as a preliminary assessment to guide future research. Method: Between January and October 2014, stool and blood samples were collected from 53 adult T1DM patients and 53 age- and gender-matched healthy individuals. Bacteroidetes and Firmicutes levels were assessed from stool sample DNA and TLR2 and TLR4 expression levels were analyzed via qPCR using RNA from EDTA blood samples from both patients and healthy controls. Results: The amounts of Bacteroidetes and Firmicutes were statistically significantly higher and lower, respectively, in the T1DM group than in the healthy control group (p < 0.001 and p < 0.001, respectively). In addition, the Firmicutes/Bacteroidetes ratios in patients with T1DM were significantly lower than in healthy controls. The TLR4 and TLR2 gene expression levels in T1DM patients were significantly upregulated and downregulated, respectively, compared to those in the control group. Conclusion: Our data are the first to show a relationship between T1DM and gut microbiota in our country. In addition, our results provide information about the connections between T1DM, gut microbiota, and TLR2 and TLR4 expression. We believe that Bacteroidetes and Firmicutes in the gut microbiota may play a role in the autoimmune process of T1DM and that these findings should be further investigated in the future. (C) 2019 Elsevier Inc All rights reserved.
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    Bruselloz Şüpheli Olgularda Brusella Seropozitifliğinin Araştırılması: Dört Yıllık Retrospektif Bir Değerlendirme
    (Logos Tıp Yayıncılığı, 2019) Taner, Zeynep Tane; Dinç, Harika Öykü; Demirci, Mehmet; Gareayaghi, Nesrin; Kurt, Aykut; Özbey, Doğukan; Tokman, Hrisi Bahar; Kocazeybek, Bekir Sami
    Amaç: Brucella cinsi bakterilerle oluşan bruselloz, sistemik bir enfeksiyon hastalığı olup dünyanın birçok ülkesinde yaygın olarak saptanmakta ve ülkemizde de oldukça sık görülmektedir. Çalışmamızın amacı, İstanbul ve çevre illerdeki yerleşim bölgelerinden dört yıllık dönemde bruselloz kuşkusu ile merkezimize başvuran 6.045 olgudan alınan serum örneklerinde bruselloz serolojik göstergelerini retrospektif olarak değerlendirmek ve sonuçları yine merkezimizde 2005-2011 yılları arasında gerçekleştirilmiş çalışmanın verileriyle karşılaştırarak değişkenlikleri irdelemektedir. Yöntem: Çalışmamıza Mart 2013- Mart 2017 tarihleri arasında İstanbul Üniversitesi-Cerrahpaşa, Cerrahpaşa Tıp Fakültesi Hastanesi Tıbbi Mikrobiyoloji Laboratuvarı Seroloji/ELISA birimine gönderilen bruselloz şüpheli olgulara ait serum örnekleri dahil edilmiştir. Örneklerden Brucella Serum Aglütinasyon (SAT), Coombs’lu Wright (CT) ve Rose-Bengal (RB) testleri yapılmıştır. Bulgular: Dört yıllık değerlendirme sonucunda, bruselloz şüpheli 6045 olgunun 107 (%1.8)’si seropozitif, 5938 (%98.2)’i seronegatif bulunmuştur. Brusella seropozitif 107 olgunun 73 (%68.2)’ü RB ve SAT ile eş zamanlı pozitif bulunmuş, 34 (%31.7) olgu ise RB ve SAT test sonuçları arasında uyumsuzluk görülmesi nedeniyle, CT sonucuna göre brusella seropozitif olarak belirlenmiştir. Brusella seropozitiflik oranı kadınlarda (%58) erkeklere (%42) göre daha yüksek olsa da istatistiksel olarak anlamlı bir fark bulunmamıştır. Olguların %28’inde aile içi aynı kaynaktan bulaş, %48’inde kırsal kesimde yaşama öyküsü saptanmıştır. Sonuç: Verilerimizin retrospektif değerlendirmesi sonucunda, bu çalışmada İstanbul ve çevre illerinde saptadığımız bruselloz seropozitiflik oranı (%1.8), aynı merkezde bir önceki dönem elde edilen orana göre (%3) düşük bulunmuştur. Bruselloz seropozitifliğinin oransal düşüklüğünde, son yıllarda görsel ve yazılı iletişim araçlarındaki artışla hayvansal kaynaklı beslenme konusunda daha bilinçli ve hijiyen kurallarına uyan insan kitlelerindeki artışın rolü olabileceğini düşünmekteyiz.
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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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    Comparison of new and classical point mutations associated with clarithromycin resistance in Helicobacter pylori strains isolated from dyspeptic patients and their effects on phenotypic clarithromycin resistance
    (Microbiology Soc, 2019) Kocazeybek, Bekir; Sakli, Merve Kutlu; Yuksel, Pelin; Demirci, Mehmet; Caliskan, Reyhan; Sarp, Tevhide Ziver; Saribas, Suat
    Purpose. We aimed to investigate the presence of three recently identified point mutations (A2115G, G2141A and A2144T) of the 23 S rRNA gene and compare them with the three most frequently encountered point mutations (A2142G, A2142C and A2143G) in Helicobacter pylori strains in Turkey. Methodology. A total of 63 patients (mean 47.08 +/- 12.27) were included. The E-test method (for clarithromycin) was used for the clarithromycin antimicrobial susceptibility test of isolated H. pylori strains. Real-time PCR was used to detect the point mutations. Results. A total of 24 out of 63 H. pylori strains (38.1%) were detected as clarithromycin resistant (>0.5 mg l(-1)). The new A2115G (n:6, 25%), A2144T (n: 7, 29.1%) and G2141A, 8 (n: 8, 33.3%) mutations and the classical A2142G (n: 8, 33.3%) and A2143G (n: 11, 45.8%) point mutations were detected in the 24 clarithromycin-resistant strains. The A2144T point mutation had the highest median MIC value (3 mg l(-1)) amongst the new mutations, but the classical mutations (A2142G and A2143G) had the highest median MIC values (256 mg l(-1)) overall. The presence of the A2115G (OR: 31.66), A2144T (OR: 36.92) or G2141A (OR: 28.16) mutations increased the likelihood of clarithromycin resistance in H. pylori strains by 31.66-, 36.92- and 28.16-fold (ORs), respectively, according to the binary logistic regression analysis. Conclusion. We concluded that classical mutations of the 23 S rRNA gene resulted in higher clarithromycin MIC values than new mutations. These new point mutations caused moderate elevations in the MIC values of clarithromycin-resistant H. pylori strains.
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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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    COVID-19 studies involving machine learning methods: A bibliometric study
    (Lippincott Williams & Wilkins, 2023) Eden, Arzu Baygul; Kayi, Alev Bakir; Erdem, Mustafa Genco; Demirci, Mehmet
    Background:Machine learning (ML) and artificial intelligence (AI) techniques are gaining popularity as effective tools for coronavirus disease of 2019 (COVID-19) research. These strategies can be used in diagnosis, prognosis, therapy, and public health management. Bibliometric analysis quantifies the quality and impact of scholarly publications. ML in COVID-19 research is the focus of this bibliometric analysis.Methods:A comprehensive literature study found ML-based COVID-19 research. Web of Science (WoS) was used for the study. The searches included machine learning, artificial intelligence, and COVID-19. To find all relevant studies, 2 reviewers searched independently. The network visualization was analyzed using VOSviewer 1.6.19.Results:In the WoS Core, the average citation count was 13.6 +/- 41.3. The main research areas were computer science, engineering, and science and technology. According to document count, Tao Huang wrote 14 studies, Fadi Al-Turjman wrote 11, and Imran Ashraf wrote 11. The US, China, and India produced the most studies and citations. The most prolific research institutions were Harvard Medical School, Huazhong University of Science and Technology, and King Abdulaziz University. In contrast, Nankai University, Oxford, and Imperial College London were the most mentioned organizations, reflecting their significant research contributions. First, Covid-19 appeared 1983 times, followed by machine learning and deep learning. The US Department of Health and Human Services funded this topic most heavily. Huang Tao, Feng Kaiyan, and Ashraf Imran pioneered bibliographic coupling.Conclusion:This study provides useful insights for academics and clinicians studying COVID-19 using ML. Through bibliometric data analysis, scholars can learn about highly recognized and productive authors and countries, as well as the publications with the most citations and keywords. New data and methodologies from the pandemic are expected to advance ML and AI modeling. It is crucial to recognize that these studies will pioneer this subject.
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    Detection Of Carbapenem-Resistant Klebsiella Pneumoniae Strains Harboring Carbapenemase, Beta-Lactamase And Quinolone Resistance Genes İn İntensive Care Unit Patients
    (Deutsche Gesellschaft für Krankenhaushygiene, 2020) Demirci, Mehmet; Ünlü, Özge
    Aim: Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) strains are important nosocomial pathogens worldwide. In this study, we aimed to reveal the antibiotic resistance of clinical CR-Kp strains and determine the presence of KPC, OXA-48, VIM and IMP carbapenemase genes. CTX-M-1, TEM-1, SHV-1 extended-spectrum beta-lactamase (ESBL) genes, qnrA, qnrB, qnrS plasmid-mediated quinolone resistance genes and sul1 and sul2 sulfonamide resistance genes provided molecular epidemiological data. Methods: A total of 175 K. pneumoniae strains were isolated from clinical samples of patients hospitalised in an intensive care unit (ICU) betweent April and October 2017. The strains were identified with conventional methods, with VITEK 2 (BioMerieux, France) and MALDI-TOF MS (Bruker, USA). Antimicrobial susceptibilities were tested using the disc-diffusion method and E-test (BioMerieux, France). Antimicrobial resistance genes were investigated via real-time PCR in strains identified as CR-Kp. Results: High frequencies of blaTEM-1 (86.36%), blaSHV-1 (86.36%), and blaCTX-M-1 (95.45%) genes were found in CR-Kp strains. Morever, all three ESBL genes coexisted in 77.3% of all strains. blaKPC was detected in 12 (54.55%) of the strains, and 4 of them which had an MIC> 16 ?g/mL to imipenem showed blaOXA-48 positivity as well. The qnrS gene determinant (86.36%) had the highest frequency, and strains carrying qnrA showed higher MICs for ciprofloxacin. Conclusion: CR-Kp strains are able to develop different antimicrobial resistance patterns according to regional changes in antimicrobial therapeutic policies. Thus, it is important to monitor the regional molecular epidemiological data for efficient treatment.
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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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    Detection Of O25b-ST131 Clone, Ctx-M-1 And CTX-M-15 Genes Via Real-Time PCR İn Escherichia Coli Strains İn Patients With Utıs Obtained From A University Hospital İn Istanbul
    (Elsevier BV, 2019) Demirci, Mehmet; Ünlü, Özge; İstanbullu Tosun, Ayşe
    Background Escherichia coli sequence type 131 is an important multidrug resistant clone responsible from more than half of ESBL-producing E.coli isolates. Aim of this study was to investigate the presence of O25b-ST131 clone, CTX-M-15 and CTX-M-1 genes in the E. coli strains isolated from both hospital and community acquired UTIs by real-time PCR and to reveal molecular epidemiological data. Methods Non-duplicate E. coli (n?=?101) strains isolated from UTI patients were included. Bacterial identifications were performed with VITEK Compact. Antimicrobial susceptibility tests, phenotypic ESBL and E-tests were performed conventionally. Real-time PCR was utilized to detect presence of O25b-ST131 clone, blaCTX-M-15 and blaCTX-M-1. Results O25b-ST131 clone, CTX-M-1 and CTX-M-15 were detected in 22%, 73%, 37% in UTIs, respectively. Presence of O25b-ST131 clones and CTX-M-1 genes among E. coli strains isolated from inpatients were found statistically higher than outpatients. The most effective choice was found to be fosfomycin and nitrofurantoin in outpatients and inpatients, respectively. The MIC90 values of Amikacin, Cefotaxime, Cefepime and Ciprofloxacin were higher in inpatients than in oupatients, whereas Cefotaxime and Ciprofloxacin MIC50 values were found to be higher in inpatients than in outpatients. The highest increase of MIC90 values was observed in O25b-ST131, CTX-M-1 and CTX-M-15 coexistence. Conclusion The presence of O25b-ST131 clone, CTX-M-1 and CTX-M-15 genes in E. coli strains in patients with UTI has been revealed. In the presence of the O25b-ST131 clone, a significant increase was observed in the ciprofloxacin MIC values indicating the importance of monitorization of the clone using molecular epidemiology.
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    Detection of staphylococcal enterotoxin genes in raw milk samples by real-time PCR
    (Agricultural Research Communication Centre, 2019) Yigin, Akin; Demirci, Mehmet; Altun, Serap Kilic; Dinc, Hikmet
    Presence of significant level of enterotoxigenic S. aureus in raw milk of sheep, goat and donkey may cause serious food borne disease. Many people worldwide, use raw milk in their daily life but data on presence of virulence genes in cow, sheep, goat and especially donkey milk seems to be very limited. For this reason, aim of this study was to determine the presence both S. aureus and nine staphylococcal enterotoxin genes in cow, sheep, goat and donkey milks. A total of 231 raw milk samples were collected from 48 cow, 65 goat, 65 sheep and 53 donkey were collected. To detect presence of S. aureus both conventional culture and real-time PCR were used and to detect nine staphylococcal enterotoxin genes directly in milk, real-time PCR was performed. Conventional culture and real-time PCR results were found to be similar for presence of S. aureus and it was detected in 52 (22.51%) out of 231 raw milk samples. Staphylococcal enterotoxin genes were detected in 27 out of 52 S.aureus positive samples and a total of 62 enterotoxin genes were detected in these samples. However enterotoxin genes could not be detected in two S. aureus positive donkey milk. Hence, real-time PCR proved to be reliable and faster than conventional methods to detect presence of enterotoxigenic S. aureus in milk. Raw milk samples from different animals many contain enterotoxigenic S. aureus. Therefore, one should be careful during raw milk consumption as enterotoxigenic S. aureus in milk may cause dangerous public health problem which need routine screening for this pathogen in milk.
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    Determination of Antifungal Activity Against Invasive Candidiasis Agents and Trace Element Content of Fig Tree Latex Samples Obtained From Trabzon Province
    (International Journal of Advances in Engineering and Pure Sciences, 2021) Ünlü, Özge; Alkan, Fatma Ateş; Özsobacı, Nural Pastacı; Özyüksel, Sedanur; Demirci, Mehmet
    Candidiasis is a major health concern causing both morbidity and mortality. The increasing prevalence of antimicrobialresistant fungi associated with life-threatening systemic mycoses, led a constant need for new antifungal agents. Herbalmedicines have been tried for this purpose for centuries. The antifungal effect of fig tree latex has been reported and some traceelements such as zinc were associated with antifungal effects. The aim of this study was to determine the trace element contentand in-vitro antifungal activity of fig tree latex sample against Candida. albicans, C. glabrata, C. tropicalis and C. krusei. Figtree latex samples were obtained from four different fig tree at Trabzon province in July 2019. The broth microdilutiontechnique was performed to investigate antifungal activity against standard Candida strains and trace elements level weredetected with Inductively Coupled Plasma Optical Emission Spectrophotometer (ICP-OES) analyzer. The most powerfulantifungal activity was reached at a concentration of 0.5 for C. albicans and C. tropicalis, and at a concentration of 0.125 forC. krusei and C. glabrata in fig tree latex. According to trace element analysis, magnesium had the highest level, followed bycalcium and phosphorus. Selenium, aluminium, lead and nickel levels were too low to be measured. As a conclusion, fig treelatex has an antifungal potential against Candida species and this may be caused by the high level of magnesium that it contains,however more studies are needed to understand the therapeutic effects of fig tree latex.
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    Diagnostic performance of the RT-qPCR method targeting 85B mRNA in the diagnosis of pulmonary Mycobacterium tuberculosis infection
    (Elsevier Science London, 2018) Demirci, Mehmet; Saribas, Suat; Ozer, Nigar; Toprak, Sezer; Caglar, Emel; Ortakoylu, Gonenc; Yuksel, Pelin
    Background: Several nucleic acid amplification techniques (IS6110, 16S rRNA, and 85B mRNA) were developed for the rapid, direct detection of Mycobacterium tuberculosis. We aimed to assess the diagnostic performance of 85B mRNA-based RT-qPCR by comparing with the real-time PCR COBAS TagMan MTB Kit while using the BACTEC MGIT 960 method as the gold standard. Methods: 60 patients with confirmed pulmonary TB and 60 individuals without TB were included as the study and control groups, respectively. Sputum specimens were cultured using LJ and BACTEC MGIT 960 systems. Extracted DNA was used for COBAS PCR in a CONAS TagMan 48 analyzer. 85B mRNA detection was performed by RT-qPCR. Results: The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of COBAS TagMan MTB Test were detected as 93.3%, 83.3%, 84.8%, 92.6%, and 88.3%, respectively. The same diagnostic parameters of RT-qPCR were: 98.3%, 95.0%, 95.2%, 98.3%, and 96.7%, respectively. According to the binary logistic regression analysis, RT-qPCR (OR: 19,924, p < 0.001) was identified as the more optimal test. Conclusion: RT-qPCR targeting the 85B gene of M. tuberculosis seems to be a more useful and rapid technique than DNA-based methods for detecting live M. tuberculosis bacilli from sputum specimens. (C) 2018 The Authors. Published by Elsevier Limited on behalf of King Saud Bin Abdulaziz University for Health Sciences.
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    Distribution of AdeABC Efflux System Genes in Acinetobacter baumannii Isolated from Blood Cultures of Hospitalized Patients and Their Relationship with Carbapenem and Aminoglycoside Resistance
    (Galenos Yayincilik, 2019) Ari, Hamza; Aydogan, Okan; Demirci, Mehmet; Cakirlar, Fatma Koksal
    Introduction: The increasing emergence of multidrug-resistant (MDR) Acinetobacter infections has become a significant challenge for physicians and clinical microbiologists owing to the difficulties arising during therapy. The major efflux mechanism associated with MDR in A. baumannii is the chromosomally encoded tripartite efflux pump, AdeABC, which has been reported worldwide. AdeABC belongs to the resistance-nodulation-division efflux pump family and has a three-component structure: AdeB forms the transmembrane component, AdeA forms the inner membrane fusion protein, and AdeC forms the outer membrane protein. AdeABC is chromosomally encoded and is regulated by a two-component system containing a sensor kinase (AdeS) and its associated response regulator (AdeR). Point mutations in these components are associated with the overexpression of AdeABC, thereby leading to multiple drug resistance. The purpose of this study was to investigate the distribution of the AdeABC efflux pump genes and their relationship with carbapenem and multiple drug resistance in A. baumannii strains isolated from the blood cultures of hospitalized patients. Materials and Methods: A total of 97 A. baumannii strains that were isolated from the blood cultures of hospitalized patients in different departments, were included in the study. The Phoenix Automated System was used to identify and determine antibiotic susceptibility patterns. The susceptibility of the study strains to carbapenems, ciprofloxacin, trimethoprim-sulfamethoxazole, amikacin, gentamicin, and netilmicin were determined according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. AdeRS mutations and adeB gene expression of drug efflux genes were analyzed by sequencing and qPCR, respectively. The 16S rRNA gene was used as a housekeeping gene, and the A. baumannii ATCC 19606 standard strain was also used to normalize the expression results of adeB gene. Results: Of the 97 isolates, 61 were found to be carbapenem resistant. The resistance rates of carbapenem-resistant A. baumannii (CRAB) isolates were found to be 100% for ceftazidime; 96.7% for cefepime, piperacillin-azobactam, ciprofloxacin, and trimethoprim-sulfamethoxazole; 86.8% for amikacin; and 75.4% for gentamicin and netilmicin. The significant overexpression (3.45-52.18 fold) of adeB was observed in 49 CRAB isolates, whereas less increased levels were observed in only 12 CRAB isolates (0.23-0.54 fold) and non-CRAB isolates (0.109-0.783 fold). In total, 80.3% of the CRAB isolates were positive for the adeRS genes. The p.Val120Ile change in the AdeR aminoacid sequence was determined in 42.8% of the adeB-overexpressing CRAB isolates. The p.His158Leu and p.Pro116Ser changes were found in 36.7% of these isolates. None of the non-CRAB isolates had p.Val120Ile, p.His158Leu, and p.Pro116Ser changes. In the AdeS aminoacid sequence, p.Gly293Ser, p.Leu105Phe, and His227Asp changes were most commonly observed in adeB-overexpressing CRAB isolates, whereas pGly293Ser change was detected in only 8% of the non-CRAB isolates. Conclusion: These data showed that AdeABC efflux pump overexpression (both adeB expression and AdeRS mutation) was higher than expected in our A. baumannii isolates. They were significantly associated with the AdeABC efflux system and both CRAB and MDR isolates. The overexpression of adeB and aminoacid changes in the AdeRS regions led to an increase resistance to different antibiotics; therefore, A. baumannii strains should be monitored to ensure the correct treatment, especially in nosocomial MDR.