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Öğe Comparison of clinical characteristics of wild-type SARS-CoV-2 and Omicron(2022) Kırca, Füsun; Aydoğan, Sibel; Gözalan, Ayşegül; Kayıpmaz, Afşin Emre; Özdemir, Fatma Ayça Edis; Tekçe, Yasemin Tezer; Beşer, İpek Omay; Gün, Pınar; Ökten, Rıza Sarper; Dinç, BediaOBJECTIVE: This study aimed to investigate the effect of mutations by comparing wild-type SARS-CoV-2 and Omicron regarding clinical features in patients with COVID-19. It also aimed to assess whether SARS-CoV-2 cycle threshold value could predict COVID-19 severity. METHODS: A total of 960 wild-type and 411 Omicron variant patients with positive results in SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction test from oropharyngeal and/or nasopharyngeal samples during their hospital admissions were included in this retrospective study. The reference symptoms of the patients were obtained from the hospital database. The correlation between chest computed tomography findings and the "cycle threshold" of patients with wild-type SARS-CoV-2 was assessed. RESULTS: Cough, fever, shortness of breath, loss of taste and smell, and diarrhea were found to be statistically significantly higher (p=0.001; 0.001; 0.001; 0.001; and 0.006; respectively) in the wild-type cohort, while in the Omicron cohort, sore throat and headache were found to be statistically significantly higher (p=0.001 and 0.003, respectively). An inverse relationship was found between chest computed tomography findings and viral load. CONCLUSION: This study revealed that the Omicron variant tended to infect predominantly the upper respiratory tract and showed decreased lung infectivity, and the disease progressed with a milder clinical course. Therefore, the study showed that the tropism of the virus was changed and the viral phenotype was affected. It was also found that SARS-CoV-2 viral load did not predict COVID-19 severity in patients with wild-type SARS-CoV-2.Öğe Distribution of Hepatitis C Virus Genotypes in Patients Diagnosed with Hepatitis C in Our Hospital: 2015-2018(2021) Hacıseyitoğlu, Demet; Sarınoğlu, Rabia Can; Gözalan, Ayşegül; Batırel, Ayşe; Söyletir, GünerIntroduction: This study aimed to investigate the distribution of hepatitis C virus (HCV) genotype and its variability in certain sociodemographics in patients with chronic hepatitis. Materials and Methods: Anti-HCV was performed by chemiluminescent micro-particle immune assay (Abbott Architect i2000SR, Germany), and HCV-RNA viral load detection was applied with real-time reverse transcriptase polymerase chain reaction (RT-PCR) in the system (Cobas AmpliPrep-Cobas TaqMan, Roche, Germany). Genotype detection was performed with RT-PCR upon with RT-PCR method in the system of Abbott RT-HCV Genotype 2 (Abbott Laboratories, USA) and with Bosphore-HCV Genotyping KitV3 in the Montania 4896 device (Anatolia Diagnostics and Biotechnology Products, Turkey). Frequency and percentage dispersions of all data obtained from patient files and laboratory information system were evaluated through the Statistical Package for the Social Sciences statistics software program. Results: HCV-RNA was positive in 628 of 2,381 patients with anti-HCV positivity (26.4%), and genotypes of 319 of which were evaluated. Mean age of 319 patients was 51.6 (standard deviation: 16.1). The most frequent genotypes were 1b (61%), 3 (19%), and 1a (10%). Incidences of genotype 1b among all genotypes between the dates of 2015-2018, were found 34.7%, 29%, 15.5% and 20.7% respectively (p=0.001). Contagion sources were medical interventions, and 1 b was the most frequent genotype. Genotype 3 was most common in patients with intravenous drug addiction. A total of 168 of 238 patients who were Turkish citizens were detected to have genotype 1 b, whereas 28 of them had genotype 3 and 25 had genotype 1a. Seventy-eight (24.7%) of the 316 patients, whose genotypes were tested, were foreigners coming mostly from Georgia, Turkmenstan, and Syria respectively. The most frequent genotype of Georgian and Turkmenistanian was 1 b and Syrian was both 1a and 4. Conclusion: This study shows the most frequent genotype to be 1b and its prevalence is statistically decreased over the years, whereae other genotypes (1a, 3, 4, 3a, 1a/3, 1b/3, c-k, 2/3, 1/4, 3/4, and 5) increased.Öğe Evaluation of antibody response after COVID?19 vaccination of healthcare workers(2022) Uysal, Elif B.; Gümüş, Sibel; Bektöre, Bayhan; Bozkurt, Hale; Gözalan, AyşegülThe common goal of all vaccines developed against COVID-19, although they have been designed with different methods, is to develop an effective immunity and antibody response against SARS-CoV-2. However, the postvaccination immune response and antibody levels differ between individuals. This study examined the relationship between postvaccine seropositivity rates, age, gender, smoking, and body mass index (BMI), and antibody titers. A total of 314 healthcare workers (HCW) who were not previously infected with COVID-19 and who had received two doses of CoronaVac inactivated vaccine participated in the study. Seropositivity against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was measured from the participants 4 weeks after the second dose of vaccine using the electrochemiluminescence (ECLIA) method. In addition, the antibody developed against the nucleocapsid protein (NCP) was evaluated and compared using Elecsys Anti-SARS-CoV-2 kit. One hundred and eighty-one of the participants were female (57.6%) with a median age of 39 (interquartile range [IQR], 10) and 133 (42.4%) were male with a median age of 41 (IQR, 11). 99.6% of the volunteers developed seropositivity 4 weeks after the second dose of vaccine. It was also observed that the rate of RBD protein antibody titer was >250 U/ml in smokers, which is quite low compared to nonsmokers (p = 0.032), and that high RBD antibody titers were proportionally lower in obese participants, according to BMI values, compared to those with normal BMI (49.5% and 9.9%). It was observed that seropositivity developed in almost all participants after the CoronaVac vaccine. However, it was determined that the antibody titer measured varied depending on factors such as smoking, BMI, and duration.Öğe Investigation of Legionella pneumophila and other Legionella species in atypical pneumonia patients(2022) Parlak, Kerim; Gözalan, Ayşegül; Aydoğan, Sibel; Koyuncu, Adem; Hasanoğlu, Hatice Canan; Nar Ötgün, Selin; Açıkgöz, Ziya CibaliObjective: The aim of this study is to investigate Legionella species in 50 patients with atypical pneumonia, using culture, urinary antigen test and molecular techniques. Methods: Non-selective BCYE-? media (Oxoid, England) and selective BMPA media (Oxoid, England) were used to isolate Legionella spp. from respiratory tract samples. The urinary samples of the patients were tested with the Alere BinaxNOW Legionella Urinary Antigen Card (Abbott, US) test to identify the presence of L. pneumophila serogroup 1 specific bacterial antigen. All respiratory tractsamples were tested with a commercial Duplic? RealTime Legionella pneumophila 23S rRNA specific region detection kit (Euroclone Diagnostica, Italy) and two home-made PCR methods. Home-made gel electrophoresis PCR tests were performed using Leg primers designed from 16S ribosomal RNA gene partial sequences for Legionella spp and primers targeting the Lmip (macrophage infectivity potentiator) gene for L. pneumophila. In the home-made real-time PCR test, primers targeting the lipopolysaccharide (lps) biosynthesis gene of L. pneumophila serogroup-1, the L. pneumophila mip gene, and the Legionella spp DNA region encoded by the 16S ribosomal RNA gene were used. Results: The commercial Real-time PCR assay identifed the sequence of L. pneumophila 23S rRNA gene specific region in seven respiratory tract samples. Five samples were detected as Legionella spp. in home-made gel electrophoresis-based PCR and home-made Real-time PCR assay. Hovewer, all samples tested negative in the urinary antigen card test for L. pneumophila serogroup 1. Conclusion: We conclude that the PCR positivities with three different molecular methods indicate that Legionella species other than L. pneumophila serogroup 1 should be investigated in the patients with atypical pneumonia using molecular methods. Also, our study demonstrates the significance of PCR methods in the investigation of Legionella species in clinical samples taken from patients with negative test results for L. pneumophila serogroup 1 specific urinary antigen test, but who are clinically considered to have Legionella pneumoniae.Öğe Molecular characterization of carbapenem-resistant Acinetobacter baumannii isolates causing bloodstream infections in intensive care unit(Refik Saydam National Public Health Agency (RSNPHA), 2020) Gözalan, Ayşegül; Ünaldı, Özlem; Kırca, Fisun; Çöplü, Nilay; Müderris, Tuba; Açıkgöz, Ziya Cibali; Durmaz, RızaObjective: In this study, the aim was to investigate the clonal relationship between carbapenem resistant Acinetobacter baumannii isolates and carbapenem resistance genes isolated from blood samples of patients followed in intensive care units by molecular methods. Methods: Bactec 9240 system (Becton Dickinson, USA) was used for the isolation of bacteria from blood culture flasks. Identification of 112 strains included in the study were performed by conventional tests, API 20NE (bioMerieux, France) and Phoenix TM 100 system (Becton Dickinson, USA) and confirmed by the presence of blaOXA-51 gene. Antimicrobial susceptibility tests were performed by Kirby-Bauer disk diffusion method and Phoenix TM 100 system. Carbapenem resistance genes; blaOXA-23, blaOXA-48, blaOXA-58, blaIMP, blaVIM and blaNDM-1 were investigated by Multiplex Polymerase Chain Reaction (PCR) method. Pulsed Field Gel Electrophoresis (PFGE) was used to determine the clonal relationship between Acinetobacter baumannii strains. Results: The antibiotic resistance percentages of strains for gentamicin, amikacin, tobramycin, netil micin, ceftazidime, trimethoprim/sulfamethoxazole, piperacillin, ciprofloxacin, ampicillin/sulbactam, piperacillin/tazobactam and cefoperazone/ sulbactam, were 88%; 81%; 78%; 36%; 98.5%; 96%; 89%; 100%; 100%; 93%; 91% respectively. MIC values of imipenem and meropenem were determined above ?8 ?g/ml in the whole group. blaOXA-51 and blaOXA-23 genes were detected in all isolates included in the study. By PFGE method, 62 different pulsotypes were detected. Among the pulsotypes, 19 of them contained ?2 strains. It was observed that 108 (96.4%) strains were clustered in 11 clonally related groups when the similarity between pulsotypes for grouping was limited to 85% or more. Conclusion: In this study, it was observed that carbapenem-resistant A. baumannii strains were resistant for all tested antibiotics at high levels except netilmicin and spread in the hospital via cross contamination. These strains posed a risk for hospital infections, however, clonal-related strains were not limited to a specific unit and time period. © 2020 Refik Saydam National Public Health Agency (RSNPHA.Öğe Reliability of antibody tests for COVID-19 diagnosis(2023) Çöplü, Nilay; Kılınç, Çetin; Gözalan, Ayşegül; Çalışır, Büşra; Sönmez, Cemile; Gül, Mustafa Mehmet; Aygün Ahlatçıoğlu, ZeynepObjective: The reverse transcription–polymerase chain reaction test (RT-PCR) is the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), and antibody tests are useful as supplemental tools for diagnosis, for measuring the population’s immunity levels, and for checking infection in asymptomatic contacts. This study aimed to evaluate the reliability of five commercial antibody detection test kits. Materials and Methods: The reliability of the Colloidal Gold COVID-19 IgG/IgM Rapid Test Kit, Antibody Rapid Test Hotgen, Beijing Hotgen Biotech Co., Ltd., China), Abbott Chemiluminescent Microparticle Immunoassay (Illinois, USA), Roche Electrochemiluminescence Immunoassay (Roche Diagnostics, Switzerland), Siemens Chemiluminescence (Munich, Germany), and Euroimmun ELISA (Lübeck, Germany) for COVID-19 diagnosis was studied. The antibody-negative group included 50 sera from 2018, and the antibody-positive group included 98 patients with positive RT-PCR results from whom blood samples had been collected 3–9 weeks after hospital discharge. Statistical analysis was performed using SPSS version 23.0 (IBM Corporation, Armonk, NY, USA). The antibody tests’ validity and intra-assay reproducibility were examined, and the Cohen’s kappa coefficients were obtained. The disease prevalence was pegged at 10%. Results: The antibody tests’ sensitivity (69.12–72.46%) and positive predictive values (42.44–100.0%) were low, and their specificity (89.58–100%) and negative predictive values (96.31–97.03%) were high. Their accuracy rates varied from 87.54% to 97.25%, and their intra-assay coefficients of variation varied from 1% to 10%. Conclusion: The agreement between the results of the antibody detection test kits was higher when the kits were classified according to the targeted antigens. The time of blood sample collection, targeted antigens, and antibody types affected the results. Serological tests were found to be useful, and the commercial kits were found to be largely reliable, although, some parameters need to be improved.Öğe Sensitivity Affected by Disease Severity and Serum Sampling Time: a Performance Evaluation of Six SARS-CoV-2 Antibody Immunoassays(2022) Şener, Burçin; Kırbaş, Ekin; Sancak, Banu; Gözalan, Ayşegül; Evren, Ebru; Karahan, Zeynep Ceren; Zeytinoğlu, Ayşın; Dinç, Bedia; Alp, Alpaslan; Dizman, Gülçin Telli; Metan, Gökhan; Birengel, Serhat; Gülten, Ezgi; Taşbakan, Meltem; Ayhan, MügeÖğe The identification of acinetobacter baumannii blood isolates by MALDI-TOF MS, ARDRA and bla(OXA-51-like) Gene-Specific Real-Time PCR(Ankara Microbiology Soc, 2020) Gözalan, Ayşegül; Aydoğan, Sibel; Hacıseyitoğlu, Demet; Kuzucu, Çiğdem; Köksal, Fatma; Açıkgöz, Ziya Cibali; Durmaz, RızaThe Acinetobacter cakoaceticus-Acinetobacter baumannii (Acb) complex consists of phenotypically very similar nosocomial species; A.baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter djikshoorniae and one environmental species Acakoaceticus. The rapid and accurate identification of the members of Acb complex is critical as these nosocomial pathogens can show differences in antimicrobial susceptibility and clinical outcomes. The conventional phenotypic methods are slow, unreliable and less efficient for the differentiation of Acb complex species, including the A.baumannii species within the Acb complex. Although various molecular methods are available, such as amplified ribosomal DNA restriction analysis (ARDRA) and bla(OXA-51-like), gene specific PCR, they are usually inconvenient for the routine diagnostic laboratories. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers an opportunity for rapid, cost-effective and convenient bacterial identification in routine diagnostic procedures conducted in clinical laboratory. In this study, we aimed to evaluate the diagnosis performance of MALDI-TOF MS system to identify blood isolates of A.baumannii. A total of 180 nonduplicate carbapenem resistant Acb complex (strain numbers; TR1-TR60) and A.baumannii (TR61-TR180) blood isolates were collected from the intensive care units of the three university hospitals in Turkey from January 2016 to December 2016. All isolates were evaluated by using bla(OXA-51-like) gene specific real time (Rt-PCR) analysis, ARDRA (restriction enzymes-AIM, Cfol, Mbol, Mspl, Rsal) method and MALDI-TOF MS (VITEK (R) MS, bioMerieux, France) system. All the strains except TRIO, TR31, TR35 and TR52 were identified as A.baumannii by ARDRA method. Out of 177 of all the isolates, presence of bla(OXA-51-like) gene was found except for TR10, TR31 and TR52 isolates. However, TR31 without the presence of bla(OXA-51-like) gene was identified as A.pittii using the ARDRA. Totally 176 isolates which were identified as A. baumannii by both of the methods, ARDRA and Rt-PCR-bla(OXA-51-like) ,were accepted as a reference for the evaluation of the diagnosis performance capacity of the MALDI-TOF MS. Overall, for all 176 isolates tested, the sensitivity obtained with the MALDI-TOF MS were 99.4% with 75% specificity. The accuracy value of the method was determined as 98.9% for the identification of A.baumannii to the species level. MALDI-TOF MS is increasingly used in diagnostic microbiology for the routine identification of bacteria to the genus, species or subspecies level with high rates of sensitivity and specificity. In future, by expanding the database, MALDI-TOF MS system would possibly become the ideal method for routine diagnostic laboratories that could potentially identify more species and even determine some characteristics of antimicrobial resistance and virulence determinants.
