Browsing by Author "SAĞLIK, İMRAN"

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Comparison of two commercial quantitative cytomegalovirus (CMV) polymerase chain reaction tests calibrated by world health organization international CMV standard
(Ankara Mikrobiyoloji, 2020-04-01) Çolak, Dilek; Sağlık, İmran; Can Sarınoğlu, Rabia; Mutlu, Derya; Peker, Bilal Olcay; Erman Daloğlu, Aylin; Parkan, Ömur Mustafa; Koyuncu Özyurt, Özlem; SAĞLIK, İMRAN; Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Mikrobiyoloji Anabilim Dalı; 0000-0003-0864-4989; GCM-3391-2022
Cytomegalovirus (CMV) viral load quantitation is important in diagnosis, follow-up, and monitoring of antiviral therapy in transplanted patients. In this study, it was aimed to compare the results of the two commercial World Health Organization (WHO) International CMV standard calibrated polymerase chain reaction tests, CMV Cobas Ampliprep/Cobas Taqman (CMV-CAP/CTM) (Roche, Germany) and Artus CMV QIASymphony-Rotorgene (CMV-QS-RGQ) (Qiagen, Germany). Both tests were performed simultaneously on 244 plasma samples. The results were measured in copies/ml and converted to IU/ml by multiplying with 0.91 for CMV-CAP/CTM and 1.64 for CMV-QS-RGQ, as specified by the manufacturers. CMV DNA was detected in 174 (71.3%) and was not detected in 52 (21.3%) of the samples and eighteen (7.4%) samples had discordant results by both of the tests. In 16 out of 18 samples with discordance, the viral load was below the dynamic measuring ranges of both tests. In one sample, CMV DNA could not be detected by CMV-CAP/CTM but detected by CMV-QS-RGQ with 497 copies/ml, and 334 copies/ ml CMV DNA was detected by CMV-CAP/CTM in another sample where it could not be detected by CMV-QS-RGQ. A high degree of agreement was found between the qualitative results of the both tests (kappa=0.80, p<0.001). For quantitative results in the dynamic measuring range of both assays (n=129), the median viral load values measured by CMV-CAP/CTM and CMV-QS-RGQ were 1140 copies/ml (range: 151-254000) and 1826 copies/ml (range: 189-551521). When the results were converted to IU/ml, the median viral load values measured by CMV-CAP/CTM and CMV-QS-RGQ were 1037 IU/ml (range: 137-231140) and 2993 IU/ml (range: 310-904133), respectively. There was a very strong correlation (r=0.94, p<0.001; r=0.94, p<0.001, respectively) between the log 10 values of the quantitative results in the dynamic measuring ranges (n= 129) as copies/ml and IU/ml of both tests. CMV-QS-RGQ values corresponding to 150, 1000, 3000 copies/ml in CMV-CAP/CTM were as 94.5, 1571, 323.5 copies/ml and CMV-QS-RGQ values corresponding to 137, 910, 2730 IU/ml in CMV CAP/CTM were as 154, 2557.6, 6965.9 IU/ml, respectively. A variation of 0.45 log(10) was determined between these values. In a total of 131 samples; 129 of them with the result of both tests in the dynamic measuring range and two of them which CMV DNA was not detected in one of the tests; it was found that 112 (85.5%) results for copy/ml, 73 (56%) results for IU/ml were within the measurement difference of +/- 0.5 log(10) and 19 (14.5%) results for copy/ml and 58 (44%) results for IU/ml were greater than +/- 0.5 log(10). Bland-Altman analysis showed that CMV-CAP/CTM test made lower measurements than CMV-QS-RGQ and the average difference for copy/ml and IU/ml results were 0.22 log(10) copies/ml and 0.47 log(10) IU/ml. In conclusion; when the results were converted to IU/ml, the number of samples with an acceptable measurement difference between the two test results (<= 0.5 log(10)) decreased and the number of samples with a measurement difference > 0.5 log(10) increased and the difference was found as statistically significant (p<0.001).Calibrating the Roche CMV CAP/CTM and Artus CMV-QS-RGQ tests with the WHO international CMV standard did not increase comparability between quantitative results in plasma samples, on the contrary, it was found that when the results were converted to IU/ml, a measurement difference indicating biologically significant viral replication was detected between the two test results.
Development and validation of a simple risk scoring system for a COVİD-19 diagnostic prediction model
(Tüberküloz ve Toraks, 2023-01-01) Güçlü, Özge Aydın; Ursavaş, Ahmet; Ocakoğlu, Gokhan; Demirdogen, Ezgi; Öztürk, Nilufer Aylin Acet; Topçu, Dilara Ömer; Terzi, Orkun Eray; Onal, Uğur; Dilektaşlı, Aslı Görek; Sağlık, İmran; Coşkun, Funda; Ediger, Dane; Uzaslan, Esra; AkalIn, Halis; Karadağ, Mehmet; AYDIN GÜÇLÜ, ÖZGE; URSAVAŞ, AHMET; OCAKOĞLU, GÖKHAN; DEMİRDÖĞEN, EZGİ; ACET ÖZTÜRK, NİLÜFER AYLİN; ÖMER TOPÇU, DİLARA; TERZİ, ORKUN ERAY; ÖNAL, UĞUR; GÖREK DİLEKTAŞLI, ASLI; SAĞLIK, İMRAN; COŞKUN, NECMİYE FUNDA; EDİGER, DANE; UZASLAN, AYŞE ESRA; AkalIn, Halis; KARADAĞ, MEHMET; Uludağ Üniversitesi/Tıp Fakültesi/Göğüs Hastalıkları Anabilim Dalı; Uludağ Üniversitesi/Tıp Fakültesi/Biyoistatistik Anabilim Dalı; Uludağ Üniversitesi/Tıp Fakültesi/Enfeksiyon Hastalıkları ve Klinik Mikrobiyoloji Anabilim Dalı; 0000-0003-1005-3205; 0000-0002-1114-6051; 0000-0002-7400-9089; 0000-0002-6375-1472; 0000-0001-7099-9647; 0000-0002-2954-4293; 0000-0001-7530-1279; 0000-0002-9027-1132; AAH-5180-2021; A-4970-2019; AAG-8744-2021; AAI-3169-2021; JCO-3678-2023; JPK-7012-2023
Introduction: In a resource-constrained situation, a clinical risk stratification system can assist in identifying individuals who are at higher risk and should be tested for COVID-19. This study aims to find a predictive scoring model to estimate the COVID-19 diagnosis.Materials and Methods: Patients who applied to the emergency pandemic clinic between April 2020 and March 2021 were enrolled in this retrospective study. At admission, demographic characteristics, symptoms, comorbid diseases, chest computed tomography (CT), and laboratory findings were all recorded. Development and validation datasets were created. The scoring system was performed using the coefficients of the odds ratios obtained from the multivariable logistic regression analysis.Results: Among 1187 patients admitted to the hospital, the median age was 58 years old (22-96), and 52.7% were male. In a multivariable analysis, typical radiological findings (OR= 8.47, CI= 5.48-13.10, p< 0.001) and dyspnea (OR= 2.85, CI= 1.71-4.74, p< 0.001) were found to be the two important risk factors for COVID-19 diagnosis, followed by myalgia (OR= 1.80, CI= 1.082.99, p= 0.023), cough (OR= 1.65, CI= 1.16-2.26, p= 0.006) and fatigue symptoms (OR= 1.57, CI= 1.06-2.30, p= 0.023). In our scoring system, dyspnea was scored as 2 points, cough as 1 point, fatigue as 1 point, myalgia as 1 point, and typical radiological findings were scored as 5 points. This scoring system had a sensitivity of 71% and a specificity of 76.3% for a cut-off value of >2, with a total score of 10 (p< 0.001).Conclusion: The predictive scoring system could accurately predict the diagnosis of COVID-19 infection, which gave clinicians a theoretical basis for devising immediate treatment options. An evaluation of the predictive
Distribution of hepatitis c virus (hcv) genotypes among intravenous drug and non-drug user patients
(Ankara Microbiology, 2021-01-01) Erman Daloglu, Aylin; Parkan, Omur Mustafa; Erdogan, Ali; Peker, Bilal Olcay; Can Sarinoglu, Rabia; Saglik, Imran; Inan, Dilara; Kuloglu, Mehmet Murat; Mutlu, Derya; Ongut, Gozde; Colak, Dilek; Saglik, Imran; SAĞLIK, İMRAN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Mikrobiyoloji Anabilim Dalı.; 0000-0003-0120-3830; 0000-0002-1071-4985; 0000-0003-0329-6778; 0000-0001-8735-2962; 0000-0001-9222-8659; 0000-0003-0864-4989; 0000-0002-6786-137X; U-8647-2019; AAX-1743-2021; AAD-7444-2022; C-7162-2016; D-7990-2018; C-9377-2018
Genotype distribution of hepatitis C virus (HCV) can vary over the years between different patient groups and regions. The prevalence of intravenous drug users (IVDU) is known to increase in our country, yet there are a limited number of studies investigating the distribution of HCV genotypes in this group. These data are essential for monitorization of the changes in HCV epidemiology. The present study aimed to evaluate the five-year results of HCV genotyping among patients infected with HCV related to IVDU and unrelated to drug use. Plasma samples of 720 patients (HCV antibody, HCV RNA positive), which were sent to our laboratory for HCV genotyping between January 2014-March 2019 were analyzed. HCV RNA extraction from plasma samples was performed in the automated-extraction system of EZ1 advanced (Qiagen, Germany) using the EZ1 virus mini kit v2.0 (Qiagen, Germany). Amplicons were obtained by amplifying the 5'NCR and core gene region in the Rotorgene 6000 real-time PCR (Qiagen, Germany) device with the HCV RNA real-time quantitative 2.0 (NLM, Italy) kit. For the genotyping, a commercial line probe assay (LIPA) based on in vitro reverse hybridization GEN-C2.0 kit (NLM, Italy) which can distinguish 1, 2, 3, 4, 6 genotypes and 1a, 1b, 2a/c, 2b, 3a, 3b, 3c, 3k, 4a, 4b, 4c/d, 4e, 4f, 4h, 5a, 6a/b, 6g, 6f/q, 6m, 7a subtypes of HCV, based on variations in the 5'-NCR and core regions was used. HCV genotype distribution of 266 IVDU (93.2%: male; median age: 25 +/- 6.82) and 454 non-drug users (51.3%: male; median age: 56.5 +/- 16.06) were examined. In order of frequency in the group with IVDU; genotype 1a, 3a, 1b, 4c/d, 2b, 4, 3 were observed and genotype 1, 2a/c and mixed genotype (1+3a) were detected in one patient. In the group without IVDU, in order of frequency; genotype 1b, 1a, 3a, 1, 2a/c, 4 were observed and genotype 2b, 4c/d, 5a, 6a/b, 6 and mixed genotype (3+4) were detected in one patient. Genotypes la and 3a were significantly higher in the IVDU group (p< 0.00001, p< 0.00001), while 1b was significantly higher in patients without IVDU (p< 0.00001). Genotypes 1a and 3a were more common in young men (p< 0.00001, p= 0.000163), while 1b was higher in middle-aged women (p< 0.00001). The incidence of genotypes 1b (p= 0.021) and 3a (p= 0.012) was higher in foreign nationals than the Turkish patients. When the HCV genotype distribution was examined by years, it was observed that the percentages of genotype 1b and la were decreasing, while the percentage of genotype 3a was increasing. As a result, in this study, HCV genotype distribution among IVDU was observed to be different from the general population without IVDU. It was found that genotypes la and 3a were more common in the IVDU group. As in the other regions of our country, genotype 1b was found most frequently in the general population. Genotype 3a increases significantly compared to years. In our study, the determination of genotypes existing in different parts of the world may be due to the foreign nationals living in our city and our region is a tourism center. It is also necessary to investigate whether there is an increase in IVDU over the years.
Effect of oral antiseptics on the viral load of sars-cov-2: A randomized controlled trial
(Wroclaw Medical Univ, 2022-07-29) Gül, Sema Nur Sevinç; Dilsiz, Alparslan; Aydın, Nurten Nur; Sağlık, İmran; SAĞLIK, İMRAN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Mikrobiyoloji Anabilim Dalı.; 0000-0003-0699-917X; 0000-0003-0864-4989; 0000-0003-4138-2490; AAD-5712-2019; A-4970-2019
Background. In the oral cavity, which plays an important role in the transmission of severe acute respira-tory syndrome coronavirus 2 (SARS-CoV-2), it is possible to reduce the viral load of SARS-CoV-2 with antiseptics, thereby minimizing the transmission of the virus during dental procedures.Objectives.The aim of this study was to clinically evaluate the effect of the hypochlorous acid (HClO) and povidone-iodine (PVP-I) solutions on the oral viral load of SARS-CoV-2.Material and methods.This randomized controlled trial was conducted on 75 patients hospitalized in the COVID-19 ward of a local hospital. All the patients included in the study were within the first 24 h of hospitalization and the first 5 days of coronavirus disease 2019 (COVID-19) symptoms. The viral load of mouthwash samples was measured with the cycle threshold (Ct) value of SARS-CoV-2 through a real-time reverse transcription polymerase chain reaction (RT-PCR). The patients were divided into 3 groups. The effect on the patient's SARS-CoV-2 viral load was investigated after gargling the mouths and throats for 30 s with HClO, PVP-I and isotonic saline. First, a sample was taken after gargling with isotonic saline, then another sample was taken after gargling for 30 s with a particular antiseptic to determine the viral load of SARS-CoV-2.Results. Comparing the before and after mouthwash samples from all 3 groups, there were no statistically significant differences in the Ctvalues before and after gargling (p > 0.05). However, there were statisti-cally significant differences in the number of negative samples after the use of HClO and PVP-I, which were positive before gargling (p < 0.05).Conclusions. In the light of the data obtained in this study, there is insufficient evidence that gargling with HClO or PVP-I reduces viral load. Taken together, these findings imply no role for antiseptics in the transmission of SARS-CoV-2 by the aerosol generated during dental procedures, or more generally, SARS-CoV-2 infection control.
Follow-up of human adenovirus viral load in pediatric hematopoietic stem cell transplant recipients
(Wiley, 2021-01-16) Peker, Bilal Olcay; Kıntrup, Gülen Tüysüz; Sağlık, İmran; Sarinoğlu, Rabia Can; Güler, Elif; Mutlu, Derya; Küpesiz, Osman Alphan; Çolak, Dilek; SAĞLIK, İMRAN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Mikrobiyoloji Anabilim Dalı.; 0000-0003-0864-4989; A-4970-2019; GCM-3391-2022
Background: The spectrum of human adenovirus (HAdV)-related disease is broad, and the virus acts on many organs and systems in hematopoietic stem cell transplantation (HSCT) recipients. We aimed to evaluate the effect of HAdV-DNA positivity with clinical and laboratory findings 4 months after HSCT.Methods and results: We retrospectively investigated HAdV-DNA in 153 HSCT recipients (<= 18 years) by quantitative real-time polymerase chain reaction (RealStar; Altona Diagnostics). The results of samples from January 2014 to December 2017 are included. HAdV-DNA was positive for at least one sample type in 50 (32.67%) patients. HAdV-DNA positivity rate was 8.92% (N: 145/1625), 40.25% (N: 64/159), and 25% (N: 2/8) for plasma, stool, and urine samples, respectively. HAdV-DNA was positive in the plasma of 38 (24.83%) patients at a median 16 (range: 1-58 days) days after HSCT. The mortality rate was 23.68% and 6.95% in plasma HAdV-positive and HAdV-negative patients (p = .014). Moreover, HAdV-DNA positivity had an impact on overall survival for allogeneic-HSCT (p = .013), with the cumulative effect including graft-versus-host disease state in multivariate analysis (p = .014).Conclusions: Plasma HAdV-DNA positivity is a potential influencer that decreases survival in the early post-transplant period. Due to the high mortality rates, close monitoring is required of HAdV infections after HSCT with sensitive methods, especially at the early stage.
Is there a role for dark field microscopy in the diagnosis of lyme disease? A narrative review
(Doc Design Informatics Co Ltd, 2023-12-01) Saraç-Pektaş, Fatma; Önal, Uğur; ÖNAL, UĞUR; Saglık, İmran; SAĞLIK, İMRAN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Mikrobiyoloji Anabilim Dalı.; JCO-3678-2023; A-4970-2019
The diagnosis of Lyme disease is becoming more common in Turkey. Nonetheless, some physicians are not aware of the diagnostic principles that should be followed when faced with a suspected patient and could use tests that are not recommended, such as darkfield microscopy. Dark field microscopy is a diagnostic technique to visualize the spirochetes that cause Lyme disease; however, it is not recommended for the diagnosis of Lyme disease. One of the main limitations of dark field microscopy is its low sensitivity. Another limitation is its high false -positivity rate, as other microorganisms and cellular debris can be mistaken for spirochetes, leading to a misdiagnosis that may result in unnecessary treatment. Therefore, this study aimed to review the literature on the role of dark field microscopy as a diagnostic method for Lyme disease and inform physicians about recommended approaches in line with the recommendations of national or international guidelines. An electronic search of Pubmed, Scopus, and Web of Science was performed using the following medical subject headings (MeSH) search terms: Lyme borreliosis, Lyme disease, Borrelia burgdorfen, diagnosis, and microscopy. With this narrative review, we aimed to inform physicians better and improve patient care for patients with suspected Lyme disease.
Prognostic factors for COVID-19 patients
(J Infection Developing Countries, 2022-03-01) Önal, Uğur; Güçlü, Özge Aydın; Akalın, Halis; Öztürk, Nilüfer Aylin Acet; Semet, Cihan; Demirdoğen, Ezgi; Dilektaşlı, Aslı Görek; Sağlık, İmran; Kazak, Esra; Özkaya, Güven; Coşkun, Funda; Ediger, Dane; Heper, Yasemin; Ursavaş, Ahmet; Yılmaz, Emel; Uzaslan, Esra; Karadağ, Mehmet; ÖNAL, UĞUR; AYDIN GÜÇLÜ, ÖZGE; AKALIN, EMİN HALİS; ACET ÖZTÜRK, NİLÜFER AYLİN; SEMET, CİHAN; DEMİRDÖĞEN, EZGİ; GÖREK DİLEKTAŞLI, ASLI; SAĞLIK, İMRAN; KAZAK, ESRA; ÖZKAYA, GÜVEN; COŞKUN, NECMİYE FUNDA; EDİGER, DANE; HEPER, YASEMİN; URSAVAŞ, AHMET; YILMAZ, EMEL; UZASLAN, AYŞE ESRA; KARADAĞ, MEHMET; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Enfeksiyon Hastalıkları ve Klinik Mikrobiyoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Göğüs Hastalıkları Anabilim Dalı.; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Mikrobiyoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Biyoistatistik Anabilim Dalı.; 0000-0001-6194-3254; 0000-0003-1005-3205; 0000-0001-7530-1279; 0000-0002-6375-1472; 0000-0002-7400-9089; 0000-0001-7099-9647; 0000-0003-0864-4989; 0000-0003-0297-846X; 0000-0003-3604-8826; 0000-0002-2954-4293; 0000-0002-3894-1231; 0000-0002-9027-1132; A-4421-2016; AAG-8459-2021; GCM-3391-2022; DTT-7416-2022; AAH-9812-2021; AEA-4817-2022; Z-1424-2019; AAU-8952-2020; AAG-9930-2019; ACQ-7832-2022; AAD-1271-2019; AAE-9142-2019; CTY-9474-2022; AAI-3169-2021; HJZ-6992-2023; CDI-1977-2022; AAG-8744-2021
Introduction: Determining prognostic factors in patients with coronavirus disease (COVID-19) can have great impact on treatment planning and follow-up strategies. Herein, we aimed to evaluate prognostic factors and clinical scores for confirmed COVID-19 patients in a tertiary care hospital in the Bursa region of Turkey. Methodology: Patients who had been diagnosed with COVID-19 microbiologically and/or radiologically between March and October 2020 in a tertiary-care university hospital were enrolled retrospectively. Adult patients (>= 18 years) with a clinical spectrum of moderate, severe, or critical illness were included. The dependent variable was 30-day mortality and logistic regression analysis was used to evaluate any variables with a significant p value (< 0.05) in univariate analysis. Results: A total of 257 patients were included in the study. The mortality rate (30-day) was 14.4%. In logistic regression analysis, higher scores on sequential organ failure assessment (SOFA) (p < 0.001, odds ratio (OR) = 1.86, 95% CI = 1.42-2.45) and CURB-65 pneumonia severity criteria (p = 0.001, OR = 2.60, 95% CI = 1.47-4.57) were found to be significant in predicting mortality at admission. In deceased patients, there were also significant differences between the baseline, day-3, day-7, and day-14 results of D-dimer (p = 0.01), ferritin (p = 0.042), leukocyte (p = 0.019), and neutrophil (p = 0.007) counts. Conclusions: In our study of COVID-19 patients, we found that high SOFA and CURB-65 scores on admission were associated with increased mortality. In addition, D-dimer, ferritin, leukocyte and neutrophil counts significantly increased after admission in patients who died.