Browsing by Author "Süer K."

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    Molecular epidemiology of hepatitis b virus in northern Cyprus; [Kuzey Kibris'ta Hepatit B Virusunun Moleküler Epidemiyolojisi]
    (Ankara Microbiology Society, 2016) Arikan A.; Şanlidaǧ T.; Süer K.; Sayan M.; Akçali S.; Güler E.
    Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, C and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (< 30 lU/ml) HBV-DNA levels, so 100 samples were included in sequence analysis. Ninety-six of those cases (13 female, 87 male; mean age: 35.51 ± 12.88 years) were anti-HBc IgG, 95 were anti-HBe and five were HBeAg positive, with a mean HBV-DNA level of 5.36 x 106 ± 3.58 x 107 lU/ml. As 32 (32%) samples yielded HBV- DNA level below the threshold of 1000 lU/ml, sequence analyses were unsuccesful, eventually 68 (68/160, 42.5%) samples could be phylogenetically analyzed. The distribution of HBV genotypes/subgenotypes were found as follows: 48 were (70.6%) D/D1; four were (5.9%) D/D2; one was (1.5%) D/D3, five were (7.4%) A/A1, two were (2.9%) A/A2 and eight were (11.8%) genotype E. Among the most frequent D1 strains, 60.4% (29/48) cases were from Turkish; single D/D3 strain from Benguela (Angola) and all eight genotype E strains were from Nigerian national cases. According to the data of this first study performed in TRNC on this subject, genotype D is dominant (53/68, 78%) in Northern Cyprus and consistent with the subgenotype distribution that is similar to Turkey and mediterranean basin. The prevalences of genotype A (7/68, 10.3%) and E (8/68, 11.8%) were also remarkable. In conclusion, although Northern Cyprus is an island country the heterogeneous distribution of HBV genotype/subgenotype may be contributed to the cosmopolitan characteristics of various populations from different countries who have come here for education, work or touristic purposes.
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    Investigation of the Correlation Between Anti-HCV Levels (S/Co) with HCV-RNA in the Diagnosis of Hepatitis C Virus (HCV) Infection; [Hepatit C Virus (HCV) Enfeksiyonunun Tanisinda Anti-HCV Duzeyi (S/Co) ile HCV-RNA Arasindaki Korelasyonun Araştirilmasi]
    (Ankara Microbiology Society, 2016) Şanlidaǧ T.; Akçall S.; Ecemiş T.; Süer K.; Erbay Dündar P.; Arikan A.; Güvenir M.; Güler E.
    Detection of borderline and/or low positive anti-HCV results by enzyme immunoassay (EIA) leads to severe problems in routine laboratories and needs confirmation with nucleic acid amplification tests which can increase the cost. In EIA tests, if the ratio of sample to cut-off (S/Co) is 2 the sample is accepted as positive according to the manufacturers' instructions. Although over the last decade the application of S/Co values have also applied to HCV-RNA readings, the current study aims to determine whether the S/Co value is adequate and applicable for the anti-HCV EIA test, and to determine whether a correlation exists between HCV-RNA and HCV infections. A total of 658 cases (402 female, 256 male; mean age: 49.4 ± 17.0 years) who were found anti-HCV positive between January 2011-July 2013 were included in the study. Anti-HCV tests were performed by chemiluminescent EIA (Architect i2000SR, Abbott, USA and LiaisonXL Murex, DiaSorin, Italy) and HCV-RNA by real-Time PCR (Cobas Ampliprep/ Cobas TaqMan HCV, Roche, USA). The mean S/Co value of the cases was 7.3 ± 4.8 (range: 1.00-17.59) and mean HCV-RNA value was 2.3x105 ± 2.1x106 copies/ml. When the anti-HCV S/Co value of varying ranges was compared with HCV-RNA readings a particular trend was noted. In the anti-HCV S/Co values of 1.0-4.0; 4.1-7.0; 7.1-10.0; 10.1-13.0; 13.1-16.0 and 316.1, HCV-RNA positivity rates were detected as 1.9%, 24.7%,37.1%, 46.7%, 56.4% and 75%, respectively. Statistical analysis indicated an intermediate positive correlation (r= 0.454) between anti-HCV ve HCV-RNA readings (p= 0.000). An adequate S/Co value was accepted as 5.0 based on the ROC analysis, and this value gave a performance confidence level of 95.6% when determining whether a patient is HCV positive. Based on the data of this study it became evident that further EIA testing is not required if the S/Co value is £ 5.0, however if the S/Co value is less than 5.0, then further clinical analysis and revaluation of the patient is required.
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    Comparing efficiency between conventional and molecular methods for detecting Legionella pneumophilia in dental unit waterline systems
    (HARD Publishing Company, 2017) İslam A.; Güvenir M.; Süer K.; Çetiner S.; Şanlıdağ T.
    The aim of our study was to detect the prevalence of Legionella pneumophilia (L. pneumophilia) in DUWLS using standard culture technique (SCT) and the real-time polymerase chain reaction (PCR) method in order to assess the risk of L. pneumophilia contamination within a dental setting. A total of 65 water samples were collected from 16 dental units and one cold water supply system from all clinical departments. L. pneumophilia could not be detected in any of the water samples using the standard SCT (0%), whereas L. pneumophilia was detected using real time PCR in three (4.6%) water samples collected from the tap system. Following the detection of L. pneumophilia, the tap systems were disinfected with surface disinfectant and water samples were recollected. The recollected water samples following disinfection were negative for L. pneumophilia once analyzed using culture and real time PCR technique. Although the culture method using BCYE media is the ‘gold standard’ for the detection of L. pneumophilia; Real Time PCR analysis may also be a quick, useful, and sensitive method for the detection of L. pneumophilia in order to control and prevent possible infections that may arise in the dental setting. © 2017, HARD Publishing Company. All rights reserved.
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    Antimicrobial activity of the essential oil of Thymus capitatus against Helicobacter pylori
    (Polish Pharmaceutical Society, 2020) Güvenir M.; Hanoğlu D.; Hano-Lu A.; Süer K.; Başer H.C.; Yavuz D.Ö.; Şalidağ T.
    Helicobacter pylori (H.pylori) is an infective agent and the main resourceful factor of chronic, active type B gastritis, peptic and duodenal ulcer, gastric carcinoma and mucosa-associated lymphoid tumors. Nowadays, pharmcological treatment of H. pylori infections attracts attention besides antibiotic treatment. The aim of this study is to analyse the chemical composition of the essential oils of Thymus capitatus and the antimicrobial activity against H. pylori. Aerial parts of wild-growing plant materials were collected during the flowering stage from three different locations. Essential oil composition analyses were performed simultaneously by GC-FID and GC-MS systems. The antimicrobial activity of the essential oil was tested by broth dilution method. The thymol percentage was determined as more than half of the essential oil composition of Thymus capitatus-Yedidalga (51.9%) and Thymus capitatus ñYıldırım (57.1%); however, the composition of thymol was 47.2% followed by 15.1% (p-cymene), 10.0% (γ-terpinene) and 5.7% (carvacrol) for Thymus capitatus-Boğaz/Girne. The essential oil from Thymus capitatus- Boğaz/Girne showed the lowest MIC and MBC values and the strongest bactericidal activity against H. pylori compared to the other tested essential oils. Bactericidal efficacy of essential oil of Thymus capitatus on H. pylori could have been affected due to the varied rates of major compounds. Thymus capitatus essential oil could be an alternative way for the treatment of H. pylori infections. © 2020 by Polish Pharmaceutical Society.
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    Evaluation of Imported Malaria Cases in Northern Cyprus between 2016 and 2019: First Data Series; [Kuzey Kıbrıs’ta 2016-2019 Yılları Arasındaki İmport Sıtma Olgularının Değerlendirilmesi: İlk Veriler]
    (Galenos Publishing House, 2020) Güler E.; Özbilgin A.; Çavuş İ.; Şanlıdağ T.; Süer K.
    Objective: In present times, malaria remains an infectious disease with a high mortality rate in some regions of the world. It is predicted to preserve its importance as a disease in the future because of the traveling human populations from malaria-endemic African countries into the regions where malaria has been eradicated. The objective of this study is to evaluate the increasing imported malaria cases in the Turkish Republic of Northern Cyprus. Methods: In this study, we investigated 13 patients who were diagnosed with malaria between 2016 and 2019. We clinically evaluated all the cases. More importantly, we made the diagnosis of these patients by Giemsa-stained thin and thick blood smears, rapid malaria antigen tests, and genotyping (only for five patients) by real-time polymerase chain reaction. Additionally, we evaluated patients with malaria in terms of age, gender, and seasons. Results: In the diagnosed malaria cases, 11 (84.4%) of them were male and 2 (15.6%) were female. There was no significance between malaria infection and gender (p=0.358). Plasmodium falciparum, Plasmodium vivax, and Plasmodium ovale infection were detected in ten patients (76.9%), two (15.4%) patients, and one (7.7%) patient, respectively. There was a significant increase (p=0.003) in the malaria cases in 2019 (n=9). The seasonal comparison revealed that malaria infections are most common in autumn (8/13, 61.5%). Conclusion: Despite the eradication of malaria in Turkish Republic of Northern Cyprus, the rising number of recently imported cases increases the risk of emerging local cases. Malaria infection should be immediately suspected, particularly, in foreign patients who travel from the malaria-endemic region and present with symptoms such as fever and shivering if the laboratory findings especially detect thrombocytopenia. © 2020 Turkish Society for Parasitology.
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    Automated Malaria Parasite Detection Using Artificial Neural Network
    (Springer Science and Business Media Deutschland GmbH, 2021) Özbilge E.; Güler E.; Güvenir M.; Şanlıdağ T.; Özbilgin A.; Süer K.
    Malaria is still an infectious disease that causes high mortality in endemic regions. It is thought that it will maintain importance in the future, especially due to people travelling from African countries where malaria is endemic to its eradicated regions. Therefore, rapid and accurate diagnosis is a critical step in the effective treatment of malaria and reducing mortality rates. This paper provides a malaria diagnosis system using an artificial neural network approach with SURF (Speeded Up Robust Features) method that helps the clinicians to predict and locate infected cell with malaria on the sample thin blood smear image. The performance of the proposed neural network and local image feature extraction technique SURF were analyzed statistically and presented in this paper. The network was trained using only 45 infected thin blood smear images and was then tested with 200 (100 infected and 100 non-infected) unseen images. The experimental results showed that the proposed system identified the malaria parasite with 93% accuracy, 86% sensitivity and 100% specificity. © 2021, The Author(s), under exclusive license to Springer Nature Switzerland AG.