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Item Should We Accept the HPV Type 66 into a Probable High-Risk Group? The Prevalence, Clinical and Histopathological Evaluation of HPV Type 66 in Gazi University, Ankara(2021) Kazanci, Ferah; Kocak, Aylin Altay; Colak, Meryem; Erdem, Ozlem; Onan, M. Anil; Bozdayi, Gulendam; 0000-0002-0451-0142; AAI-8012-2021Introduction: The prevalence of infection by different genotypes of human papillomavirus (HPV) varies among different geographic areas. The objective of the study is to determine the prevalence and distribution of HPV66 genotype among women with normal or abnormal Pap smear tests. Methods: This retrospective study was conducted in a tertiary care university hospital between January 2017 and February 2018, in central Anatolia of Turkey. This study included 288 women, 66 (%22.9) of whom had HPV DNA positive. HPV DNA screening was done by an automatized system using real time PCR method (Cobas 4800 System, Roche Diagnostics Ltd, Switzerland) and this method distinguishes types 16 and 18, while the other 12 oncogene types are reported as high-risk HPV (HR-HPV: 31,33,35,39,45,51,52,56,58,59,66,68). For the genotyping of other oncogene types, a commercial real time PCR method (NLM Genotypes 14 Real-TM Quant, NLM Diagnostic, Italy) was used. Results: The most common identified HPV types were HPV16 (%6.3), HPV 56 (%3.8), HPV 18(%3.1), HPV 66 (%3.1), HPV 51 (%2.8), HPV 52(%2.1). HPV type 66 which has admitted recently other-subtypes with their unclear oncogenicity is the third most identified type in our study. In our study 9 (%3.1) women had type 66 and 2 (%0.7) of whom had abnormal Pap smear results. One patient with syphilis whose pap smear test results was ASC-H/HSIL was evaluated by colposcopic examination and LEEP (Loop Electrosurgical Excision Procedure) and ECC (Endocervical Curettage) were performed. The result of histopatological report was benign. The other patient whose Pap smear test result was LSIL evaluated by colposcopic examination and found no pathological finding. Conclusion: The frequency of HPV 66 infection was found to be higher in our study compared to previous reports. In 2 patients out of 9 cases (% 2.4) who were detected HPV 66 had normal pap test results.Item Antibacterial Resistance in Lower Respiratory Tract Bacterial Pathogens: A Multicenter Analysis from Turkey(2021) Guclu, Aylin Uskudar; Kocak, Aylin Altay; Ok, Mehtap Akcil; Tutluoglu, Bulent; Basustaoglu, Ahmet; 0000-0002-1872-028X; 0000-0002-0451-0142; 33690209; AAU-6196-2020; AAI-8012-2021Introduction: This study aimed to evaluate the etiology of lower respiratory tract infections (LRTIs) and their antibiotic resistance. Methodology: Bacterial culture results of LRT samples from 17 hospitals between 2016-2019 were included in the study. All isolates were identified and AST were performed by automated microbiology systems. AST was performed according to EUCAST. Results: Non-duplicate 30,051 (26,890 HA and 3156 CA) isolates detected as causative pathogen. LRTIs are caused by 85.1% Gram-negative bacterial pathogens and 14.9% Gram-positive. The most common isolates among HA pathogens were Acinetobacter spp. (27.4%), P. aeruginosa (22.2%), K. pneumoniae (17.9%); among CA pathogen S. pneumoniae (19.9%), P. aeruginosa (18.9%), H. influenzae (14.6%). ESBL rate was 62.5% in K. penumoniae; 53.1% in E.coli; 19.1% in Klebsiella spp; 13.9% in Enterobacter spp.; 8.6% in Proteus spp.; 6.3% in Citrobacter spp.; and 4.3% in Serratia spp. Resistance rates to carbapenems and colistin were 92.8% and 12.8% in A baumannii, 39.8% and 7.5% in P. aeruginosa, 47.3% and 18.5% in K. penumoniae. Among staphylococci, 27.3% of S. aureus and 82.4% of CoNS were methicillin resistant. 7.6% of E.faecium and 0.9% of E. faecalis were vancomycin resistant. Linezolid resistant S. aureus, CoNS, E. faecalis and E. faecium rates were 0.3%, 2.9%, 0.0% and 4.6%. Inducible clindamycin resistant rate was 17.2% in S. aureus 38.2% in CoNS. Non-susceptible S. pneumoniae isolate rate to penicillin was 37.0%. 6.5% of S. maltophilia and 4.4% of B. cepacia isolates were resistant to trimethoprim/sulfamethoxazole. Conclusions: Antibiotic resistance was mainly observed among A. baumannii and K. pneumoniae and continuous surveillance of antimicrobial resistance patterns in the management of LRTIs is important.Item Investigation of Group A Rotavirus G10, G12 Genotypes Emerging in Patients with Acute Gastroenteritis in a Tertiary Care Hospital(2021) Kahraman, Hande; Kocak, Aylin Altay; Albakkour, Katren; Muftah, Hager; Dalgic, Buket; Caglar, Kayhan; Ahmed, Kamruddin; Bozdayi, Gulendam; 34666655Rotaviruses are the most common cause of viral gastroenteritis with the highest mortality and morbidity rates in children aged 0-5 years. The aim of this study was to determine the frequency of rotavirus infection in patients whose stool samples were sent to microbiology laboratory to investigate the etiology of diarrhea, to investigate the rotavirus genotypes that are common in our region and G10, G12 genotypes that have recently become common in the world. Fecal samples of 476 patients aged between 0-92 years who applied between November 2016 and February 2018 were studied via immunochromatographic rapid test and enzyme-linked immunosorbent assay (ELISA) methods. ELISA positive samples were studied by nested reverse transcriptase chain reaction (RT-PCR) and genotyped by agarose gel electrophoresis. Rotavirus was found positive in 18.3% and 17% of stool samples by immunochromatographic test and ELISA, respectively. All ELISA positive samples were also detected as positive by RT-PCR. 18.5% of female patients and 15.7% of male patients were found to be positive and rotavirus positivity was not statistically significant between genders. The frequency of rotavirus in different age groups was 23.5% (6-12 years), 17.3% (13-24 months) and 16% (25-36 months). It was determined that rotavirus cases were most common in the spring. G1, G2, G3, G4, G9, G10, and G12 were detected in 37%, 7.4%, 16.1%, 6.2%, 9.9%, 2.5%, 26% of the samples, respectively. G12 was the most common genotype after G1. The most common G and P genotype combination was G1P[8] (17.2%). This was followed by G12P[8] (11.11%) and G3P[8] (11.11%). P[8] (53%) was found to be the dominant P genotype. In this study, it was observed that rotavirus, which is the cause of childhood diarrhea, can also be encountered in advanced ages and even new genotypes that infect humans worldwide may also be the causative agents. Therefore, we concluded that it is important to investigate new genotypes such as G10 and G12 in molecular epidemiological studies.Item Investigation of the Rotavirus Genotypes Isolated From Patients With Acute Gastroenteritis and the Increase of G9 Type(2021) Kocak, Aylin AltayIntroduction: Rotavirus (RV) is the most common cause of gastroenteritis in children and is one of the most common cause of mortality and morbidity in developing countries. The aim of this study was to determine the genotypes of RV rapid test antigen positive patients between 0-65 years old with acute gastroenteritis attended to a tertiary care hospital in Ankara. Materials and Methods: This study was conducted between January 2013 and April 2018 at Gazi University Faculty of Medicine, Department of Microbiology, Stool samples were collected from 87 (40 female, 47 male) patients aged between 0-65 years who had gastroenteritis were sent to microbiology laboratory. RV VP-7 amplification was performed using Beg9 and End9 primers and specific primers for G typing G1-G4 and G9. VP-4 amplification was performed using con-2 and con-3 primers. P types were determined by specific primers for P[4], P[6], P[8] and P[9]. Access Quick RT-PCR (Promega Corporation, Madison, WI) was used for VP4 and VP7 gene amplification, and PCR Mastermix (Promega, Madison, WI) was used for genotyping. Results: No statistically significant difference was found between the gender of patients with positivity of RV antigen. RV infection was most common in children aged 12-23 months. Antigen positivity was most common in winter and autumn. Genotypes G1 (25.80%), G2 (3.22%), G3 (4.30%), G4 (6.45%), G9 (60.21%) constituted G types. P4 (1.14%), P8 (93.10%), P6 (5.74%) constituted P types. The combination of G and P types was the most prevalent for G9P[8] (56.98%) and G1P[8] (22.58%). Conclusion: It has been observed that G9 and P[8] are common genotypes in cases with RV infection in Ankara as in the whole world. Similar to various studies in Turkey, genotype G9P[8] had the highest ratio in the present study. Therefore, these data should be considered in RV vaccine strategies.Item In vitro activity of ceftolozane-tazobactam and ceftazidime-avibactam against clinical isolates of meropenem-non-susceptible Pseudomonas aeruginosa: A two-centre study(2020) Mirza, Hasan Cenk; Hortac, Elvan; Kocak, Aylin Altay; Demirkaya, M. Hamiyet; Yayla, Buket; Guclu, Aylin Uskudar; Bustaoglu, Ahmet; 0000-0002-1872-028X; 0000-0002-8853-3893; 0000-0002-0451-0142; 0000-0002-4335-6897; 31568882; AAU-6196-2020; F-1232-2015; AAI-8012-2021Objectives: This study aimed to compare the activity of ceftazidime-avibactam (C/A), ceftolozane-tazobactam (C/T) and three anti-pseudomonal beta-lactams (piperacillin-tazobactam, ceftazidime and cefepime) against a collection of meropenem-non-susceptible Pseudomonas aeruginosa (P. aeruginosa) clinical isolates recovered from two centres in Turkey. Methods: A total of 102 unique patient isolates of meropenem-non-susceptible P. aeruginosa were included in the study. MICs of antimicrobials were determined by the gradient diffusion method. Results: Overall susceptibility rates for C/A and C/T were 83.3% and 82.4%, respectively. Both C/A and C/T had better activity than any one of the three anti-pseudomonal beta-lactams. According to the MIC50 values, C/T was the most potent agent against isolates. Although the susceptibility rates of isolates to C/T and C/A were similar, C/T (MIC50, 1 mg/mL) was four-fold more potent than C/A (MIC50, 4 mg/mL). The MIC50 values of C/A and C/T for the isolates that were non-susceptible to three beta-lactams were significantly higher than those for isolates that were non-susceptible to zero, one or two beta-lactams. Also, the C/A MIC50 value for the isolates that were non-susceptible to two beta-lactams was higher than that for isolates which were non-susceptible to one beta-lactam. Conclusions: C/A and C/T showed good activity against meropenem-non-susceptible P. aeruginosa isolates. However, resistance to these agents was not uncommon among these isolates. The overall beta-lactam susceptibility profile of isolates seems to have an effect on the probability of susceptibility to C/A and C/T. Antimicrobial susceptibility testing should be performed for C/A and C/T if these agents are considered for treatment of infections caused by meropenem-non-susceptible P. aeruginosa. (C) 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd.Item Investigation of JC Virus Positivity By Real-time Polymerase Chain Reaction in Patients with Hematopoietic Stem Cell Transplant(2020) Colak, Meryem; Kocak, Aylin Altay; Kaynar, Lale Aydin; Ozkurt, Zubeyde Nur; Yegin, Zeynep Arzu; Bozdayi, Gulendam; 0000-0002-0451-0142; AAI-8012-2021Introduction: In immunocompromised hosts, JC virus (JCV) can reactivate and cause a lytic infection of oligodendrocytes, resulting in progressive multifocal leukoencephalopathy (PML). Bone marrow is an important reservoir and possible site of neurotropic transformation for JCV. The aim of this retrospective study was to investigate the prevalance of JCV infection by real-time polymerase chain reaction (PCR) in patients sent from bone marrow transplant service to the laboratory in our hospital. Materials and Methods: A total of 153 clinical samples obtained from 62 patients with hematopoietic stem cell transplant between December 2013 and April 2018 were included into the study. Viral nucleic acids were extracted from the samples with QIAamp DSP Virus Kit in EZ1 Advanced (Qiagen, Germany) device. Isolated viral DNA was amplified with Real Star (R) JCV PCR Kit in Rotor-GeneQ (Altona, Germany) and JCV DNA was detected with qualitative method. Results: Sixty-two patients, 35 (56.5%) males and 27 (43.5%) females, between 18 years and 71 years of age were included into the study. Total JCV DNA positivity rate was found as 11.1% (17/153). Patients' diagnosis was respectively as follows: 45.2% acute myeloid leukemia, 19.4% acute lymphoblastic leukemia, 9.7% multiple myeloma. 6.4% myeloblastic sendrome, 6.4% non-Hodgkin lymphoma, 6.4% Hodgkin lymphoma, and 6.4% anemia. The distribution of JCV DNA positivity rates was found respectively as 40% acute myeloid leukemia, 30% multiple myeloma, 10% Hodgkin lymphoma, 10% acute lymphoblastic leukemia and 10% Non-hodgkin lymphoma. It was observed that 50% of JCV DNA positive patients died in the follow-up period after hematopoietic stem cell transplantation. Conclusion: It is not possible to diagnose JCV infections clinically because they are usually asymptomatic. However, up to 90% of those diagnosed with PML die within the first six months receiving a diagnosis. Detection and clinical surveillance JCV DNA by real-time PCR for hematopoietic stem cell transplantation patients is important for early diagnosis and treatment.Item Emergence of rotavirus G9 in 2012, as the dominant genotype in Turkish children with diarrhea, in a university hospital in Ankara(2019) Kocak, Aylin Altay; Aydin, Merve; Matsumoto, Takashi; Yahiro, Takaaki; Dalgic, Buket; Bozdayi, Gulendam; Ahmed, KamruddinIntroduction: Rotavirus infection is a major cause of morbidity and mortality in infants and young children with diarrhea throughout the world. Material and Methods: In this study, we aimed to determine the detection rate of rotavirus infection in 181 children less than 5 years of age presenting with acute gastroenteritis and admitted to a tertiary care hospital in Ankara, Turkey, from April to November 2012. We documented the epidemiological data by elucidating the prevalent genotypes. Stool specimens were collected, and rotavirus antigen in the samples was detected using ELISA. G and P genotypes were determined by RT-PCR via type specific primers. The nucleotide sequence of the concerned genes was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Results: Of the 181 samples, 28 (15.5%) were positive for the rotavirus antigen. Twenty-seven samples were positive for G genotypes and 21 were positive for P genotypes. Genotypes G1 (7.1%), G2 (7.1%), G3 (7.1%), G4 (3.6%), G9 (71.5%) and P4 (3.6%), P8 (71.4%) were identified. Genotype G9P[8] (50%) was predominant in the combination of G and P genotypes. Most of the G9 strains of this study formed an independent cluster in Lineage III, except two strains which clustered with an Ethiopian G9 strain of 2012. Conclusions: It seems that during 2012 season, genotype G9P[8] increased significantly in Ankara due to a new circulating strain of G9.Item Evaluation of the results of MOTAKK hepatitis C virus RNA genotyping and hepatitis delta virus external quality assessment programs during 2015-2016(2019) Kocak, Aylin Altay; 31767550Background/Aims: To evaluate the HCV RNA genotyping and HDV RNA tests that are performed in molecular microbiology laboratories in Turkey as part of a national external quality assessment programme, MOTAKK (Molekuler Tanida Kalite Kontrol) (English translation: Quality control in molecular diagnostics). Materials and Methods: Plasmas having different HCV RNA genotypes were used to prepare HCV genotype control sera. The HDV RNA main stock was prepared from patients with chronic delta hepatitis who had a significant amount of viral load detected, as per the WHO reference materials on viral load studies that were compiled for the purpose of developing HDV RNA control sera. Samples with different viral loads were prepared from this main stock by dilution. The prepared controls were delivered to the registered laboratories. The laboratories carried out the relevant tests and entered their results via the MOTAKK web page. External quality assessment (EQA) reports of the participants were uploaded to the website as well. Results: In total, there were 23 participating laboratories, out of which 20 exclusively performed HCV genotyping, and 15 and 16 only performed HDV RNA in 2015 and 2016, respectively. The success rate of the results of the HCV genotype was 56-96% in 2015 and 30-95% in 2016. The tube with a 30% success rate had a recombinant type of HCV, therefore, it could not be detected in most of the laboratories. The HDV RNA results were evaluated qualitatively. Accordingly, HDV RNA detection rates of participant laboratories were 71-100% in 2015 and 50-100% in 2016. Conclusion: This study was the first national external quality control program in Turkey regarding HCV RNA genotyping and HDV RNA in the field of molecular microbiology, and it was implemented successfully.