Person: AĞCA, HARUN
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AĞCA
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HARUN
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Publication Viral and atypical bacterial respiratory infections in a university teaching hospital(Natl Inst Infectious Diseases, 2019-09-01) Harun, Ağca; Beyza, Ener; AĞCA, HARUN; ENER, BEYZA; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Mikrobiyoloji Anabilim Dalı; 0000-0002-2651-2034; AAH-4027-2021; ISU-9626-2023Respiratory viral and atypical bacterial agents lead to infections in a large spectrum, from mild symptoms to respiratory failure. In the present study, we aimed to detect multiple viral and bacterial agents in the respiratory samples of inpatients by real-time polymerase chain reaction (RT-PCR). Nasopharyngeal swabs and broncho-alveolar lavage samples from inpatients with respiratory infection symptoms at the Uludag University Hospital between December 1, 2015 and March 31,2018 were investigated. DNA/RNA was extracted using the EZ1 Virus Mini Kit v2.0 (Qiagen, Belgium) with the EZ1 extraction device (Qiagen, Belgium). The R-GENE (R) RT-PCR (Biomerioux, France) kit was used to detect influenza A, influenza B, respiratory syncytial virus (RSV), human metapneumovirus, rhinovirus/enterovirus (RV/EV), adenovirus, human bocavirus (hBoV), corona virus, parainfluenza virus, Chlamydia pneumoniae/Mycoplasma pneumoniae, and Legionella pneumophila in Rotor-Gene Q (Qiagen, Belgium). Patients were aged between 0 and 90 years. Overall, 177 (56.9%) patients were men and 134 (43.1%) were women. A total of 311 samples were analyzed, of which 214 (68.8%) were positive. In total, 360 agents, including 338 viruses and 22 bacteria, were detected. The commonest agents were influenza A+B (n = 65, 18,1%), hBoV (n = 64, 17.8%), RV/EV (n = 56, 15.6%), and RSV (n = 47, 13.1%). Rapid diagnosis of viral infections by RT-PCR is important for the specific treatment of patients.Publication Evaluation of 2015-2016 MOTAKK HBV DNA and HCV RNA external quality assessment national program results(Ankara Mikrobiyoloji Kulübü, 2018-10-01) Karataylı, Ersin; Soydemir, Ege; Aksoy, Zeynep Buşra; Kızılpınar, Mehtap; Altay Kocak, Aylin; Karataylı, Senem Ceren; Yurdcu, Esra; Yıldırım, Umut; Guriz, Haluk; Bozdayı, Gülendam; Yurdaydın, Cihan; İlhan, Osman; Yıldırım, Yasin; Bozdayı, A. Mithat; Oğuz, Acelya Yalçıntaş; Barış, Ahmet; Alp, Alpaslan; Aksözek, Alper; Sayıner, Arzu; Karagül, Aydan; Ordu, Aylin; İstanbullu, Aye; Otlu, Barış; Arıdoğan, Buket; Aksu, Burak; Buruk, C. Kurtuluş; Karahan, Ceren; Güney, Çakır; Toksöz, Devrim; Yıldırım, Dilara; Çolak, Dilek; Dağlar, Duygu Eren; Fındık, Duygu; Kas, Elif; Calışkan, Emel; Zeyrek, Fadile Yıldız; Arslan, Fatma; Demir, Feyza; Milletli, Fikriye; Kibar, Filiz; Özdinçer, Furkan; Dündar, Gülnür; Arslan, Hande; Ağça, Harun; Aliskan, Hikmet Eda; Güdücuoğlu, Hüseyin; Fidan, Işıl; Akyar, Isin; Afsar, Ilhan; Kaleli, İlknur; Dönmez, İsmail; YanIk, Kemalettin; Midilli, Kenan; çubukcu, Kivanc; Özdemir, Mehmet; Acar, Melek; Yalinay, Meltem; Kuşkucu, Mert Ahmet; Bakırcı, Mustafa Zahir; Aydın, Neriman; Yılmaz, Neziha; Çeken, Nihan; Ziyade, Nihan; Yılmaz, Nisel; Özgümüş, Osman Birol; Gitmişoğlu, Özlem; Demirgan, Recep; Kesli, Recep; Güçkan, Rıdvan; Sertoz, Ruchan; Akgün, Sadık; Aksaray, Sebahat; Tezcan, Seda; Kaygusuz, Sedat; Gökahmetoğlu, Selma; Meşe, Sevim; Bayik, Seyit Ahmet; Akcalı, Sinem; Gürcan, Saban; Karsligil, Tekin; Us, Tercan; Özekinci, Tuncer; Pilgir, Tulin; Aslan, Uğur; Dinc, Ugur; Coşkun, Umut Safiye Say; Çetinkol, Yeliz; Keskin, Yusuf; Ayaydın, Zeynep; Toraman, Zulal Asçı; MOTAKK HBV HCV Calisma Grubu; AĞCA, HARUN; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Mikrobiyoloji Anabilim Dalı; 0000-0002-2651-2034; ISU-9626-2023MOTAKK, as a national external quality control program has been launched to evaluate the molecular detection of viral infections including HBV DNA and HCV RNA in molecular microbiology diagnostic laboratories in Turkey. This program is prepared in compliance with ISO 17043:2010 (Conformity assessment general requirements for proficiency testing) standards, and aims to take the place of external quality control programs from abroad, contributing to standardization and accuracy of molecular diagnostic tests in our country. The aim of this study was to evaluate 2015 and 2016 results of the MOTAKK External Quality Control Program for HBV DNA and HCV RNA viral load. The calls were announced on the web page of MOTAKK (www.motakk.org). The quality control samples were sent to participating laboratories in 2015 and 2016. Main stocks were prepared from patients with chronic hepatitis B and C who had viral load detection with reference methods according to WHO reference materials for viral load studies to improve quality control sera. From these main stocks, samples with different viral loads were prepared from dilutions of plasma with HBV, HCV, HAV, HIV, Parvovirus B19 and CMV negative serologic markers. Quality control samples were sent to the participating laboratories along with the negative samples in the cold chain. The laboratories accomplished the related tests within 2-3 weeks and entered their results on the MOTAKK web page. These results were analysed according to ISO 13528 (Statistical methods for use in proficiency testing by interlaboratory comparison) and scoring reports were created by a software developed by MOTAKK and sent to participating labs. Each laboratory evaluated their own results in comparison with the other laboratory results, reassessed the tests via observing the distance from the mean result and the reference values. The number of laboratories participating in the HBV DNA and HCV RNA external quality control program was 70-73 in 2015-2016. Participants were able to comply with the program tools, registering, entering results and receiving the results reports problem. In HBV panel, 72.6-89.1% and 84.7-90.3% of the participant laboratories were in 1 standard deviation (SD) in 2015-2016, respectively. In HCV panel, 70.8-89.1% and 84.7-90.3% of the participant laboratories were in 1 SD in 2015-2016, respectively. A national external quality control program for HBV DNA and HCV RNA in Turkey has been prepared for the first time with this project and implemented successfully. All the data provided in the MOTAKK external quality control program final report, compensate all the data provided by the quality control program final reports from abroad; additionally, the report allows comparison of used technologies and commercial products.Publication Development of a real-time polymerase chain reaction method for the identification of Candida species(Ankara Microbiology, 2015-01-01) Ağca, Harun; Cilo, Burcu Dalyan; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; Ener, Beyza; AĞCA, HARUN; Cilo, Burcu Dalyan; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; ENER, BEYZA; Uludağ Üniversitesi/Tıp Fakültesi/Tıbbi Mikrobiyoloji Anabilim Dalı.; 0000-0002-2651-2034; AAG-8523-2021; AAH-4027-2021; IVV-5845-2023; ISU-9626-2023; KLD-2582-2024Candida species are one of the major causes of nosocomial infections and are the fourth most common agent involved in bloodstream infections. The impact of non-albicans Candida species is increasing, however C.albicans is still the most common species. Since the antifungal susceptibility pattern among Candida spp. may be different, rapid diagnosis and identification of non-albicans Candida spp. are important for the determination of antifungal agents that will be used for treatment. The aim of the study was to describe a real-time polymerase chain reaction (Rt-PCR) assay that rapidly detects, identifies and quantitates Candida species from blood culture samples. A total of 50 consecutive positive blood culture bottles (BACTEC, Beckton Dickinson, USA) identified at our laboratory between June-November 2013, were included in the study. Reference strains of Candida spp. (C.albicans ATCC 10231, C.glabrata ATCC 90030, C.tropicalis ATCC 1021, C.krusei ATCC 6258, C.parapsilosis ATCC 22019 and C. dubliniensis CD36) grown on Sabouraud dextrose agar were used for quality control. BACTEC bottles that were positive for Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were also studied to search the cross-reactivity. A commercial kit (Zymo Research, USA) was used for DNA extraction. Real-time PCR was performed on LightCycler 480 (Roche, Germany) with primers and probes specific for 18S rRNA of Candida species. Twenty microlitres of the reaction mix contained 2 mu l of extracted DNA, 2 mu l of LightCycler Fast Start DNA Master Probe (Roche Diagnostics, Germany), 2 mu l of MgCl2 (5 mmol), 2 mu l of 10x PCR buffer (Roche Diagnostics, Germany), 0.5 mu l of each primer (0.01 nmol/mu l) and 1 mu l of each probe (0.1 mu mol/mu l) (TibMolBiol, Germany). Amplification was performed using the following conditions; 95 degrees C for 10 mins and 50 cycles of denaturation at 95 degrees C for 10 secs, annealing at 62 degrees C for 10 secs and polymerisation at 72 degrees C for 20 secs. A melting curve was created by cooling the producs at 50 degrees C for 30 secs and then heating to 80 C at a rate of 0.1 degrees C/sec measuring of the fluorescence simultaneously. For the quantitation of fungal DNA according to the standard curve, serial dilutions of C.albicans ATCC 10231 DNA from 3 x 10(5) to 3 x 10(2) ng/mu l were used. All of the strains were also identified by conventional methods and sequence analysis in order to compare the results obtained by Rt-PCR. In our study, all patient and standard samples could be amplified, identified and quantitated by this developed Rt-PCR method. A total of 50 strains, of them 26 were C.parapsilosis, 15 were C.glabrata, 6 were C.albicans, and 3 were C.tropicalis have been detected and identified among patient samples. The results were completely concordant with the sequencing and conventional methods, so the sensitivity and specificity of this method were estimated as 100 percent. In conclusion, it was novel Rt-PCR developed and evaluated in this study is considered as a rapid, accurate, reproducible, sensitive and specific method for the detection, identification and quantitation of commonly observed Candida spp. strains.Publication Conventional culture and molecular screening methods for detection of vancomycin-resistant enterococci activity(Carbone Editore, 2016-01-01) Karakecili, Faruk; Cilo, Burcu Dalyan; Akın, Hicran; Ağca, Harun; Sınırtaş, Melda; Özakın, Cüneyt; Yılmaz, Emel; Akalın, Halis; Cilo, Burcu Dalyan; Akın, Hicran; AĞCA, HARUN; Sınırtaş, Melda; ÖZAKIN, CÜNEYT; YILMAZ, EMEL; AKALIN, EMİN HALİS; Uludağ Üniversitesi/Tıp Fakültesi/Microbiooji Bölümü; 0000-0002-7368-7187; 0000-0002-2651-2034; 0000-0002-3894-1231; 0000-0001-7530-1279; IVV-5845-2023; AAH-4027-2021; AAU-8952-2020; AAG-8392-2021; ISU-9626-2023Introduction: Early identification of vancomycin-resistant enterococci (VRE) colonization by screening patients is necessary in tends of preventing spread and development of infection. The purpose of this study was to investigate the presence of VRE using and real time polymerase chain reaction (RT-PCR) and to compare the results and costs.Materials and methods: Patients in the risk group attending our hospital and planned for treatment with hospitalization were included. Two rectal swab specimens were taken. One swab specimen was inoculated into enterococci broth for CCSM. Resistant gene investigation was performed with the other specimen by using RT-PCR. The costs of the two methods were then compared.Results: VRE were detected in 75 (6.63%) of the 1130 patients screened using the two methods. Resistance gene was determined in 69 (6.1%) patients using RT-PCR and 32 (2.8%) with CCSM. RT-PCR results were negative in 6 patients with VRE growth determined using CCSM. VRE was detected with CCSM in all 26 patients in whom vanA genotype VRE were determined using RT-PCR, but no growth was determined with CCSM in any of the 43 patients in whom vanB genotype VRE were detected. Results obtained in 3 days using CCSM and within 4 hours using RT-PCR. Costs were 58 $ with CCSM and 46 $ with RT-PCR.Conclusion: VRE colonization being detected faster with RT-PCR than CCSM. When the costs in isolation of patients until VRE screening test results emerged were compared, VRE screening with RT-PCR was cost-effective. RT-PCR was markedly superior to CCSM in determining VanB type resistance. Due to the late results from CCSM and its failure to detect VanB type resistance, we think that RT-PCR can be an alternative to CCSM or that the two techniques can usefully be combined depending on the hospital conditions.