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Introduction: 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.

Background/Aim: The frequency and severity of respiratory tract infections increase with aging. The aim of this study was to determine the bacterial profile of respiratory tract samples in geriatric patients and evaluate the antibiotic susceptibility patterns of the pathogens. Methods: In this cross-sectional study, a total of 509 clinical samples which were obtained from 302 geriatric patients over 65 years of age and sent to the microbiology laboratory between June 2019-January 2021 were investigated retrospectively. The identification and antibiotic susceptibilities of strains were evaluated with BD-Phoenix-100 fully automated microbiology system. Results: Of the 302 geriatric patients, 166 (%55) were males and 136 (%45) were females. The most isolated pathogens were Klebsiella pneumoniae (25.3%) Pseudomonas aeruginosa (22.5%) and Acinetobacter baumannii (10.2%), Corynebacterium striatum (7.3%), Escherichia coli (6.4%), Staphylococcus aureus (6.4%) and coagulase-negative staphylococci (4.2%). The production of ESBL in Klebsiella pneumoniae strains (52.3%) was higher than in Escherichia coli (41%) strains. All Corynebacterium striatum samples were resistant to ciprofloxacin, tetracycline, rifampin, and penicillin. Methicillin resistance among Staphylococcus aureus (MRSA) isolates was 22.7% and they were 100% susceptible to vancomycin and teicoplanin. Above 90% of K. pneumoniae, P. aeruginosa and A. baumannii positive patients were hospitalized in intensive care units (P

It is important to understand the frequency of Human Papilloma Virus (HPV) and the factors associated with HPV infections, to determine prevention, control and measures to be taken. In this study, it was aimed to investigate the HPV prevalence, genotype distribution and possible risk factors in women applying to the Family Health Center. Sexually active, clinically asymptomatic fifty women aged 30-65 who applied to Safranbolu Family Health Center between October 2018 and March 2019 were included in the study. In order to compare HPV-DNA positivity and socio-demographic characteristics, the education status, number of pregnancies, age of first sexual intercourse, presence of chronic disease, pap smear test and HPV vaccine status, etc. information was recorded and cervical swab samples were taken for detection of HPV-DNA. Viral DNA was isolated with the QIAamp® Viral DNA Kit (QIAGEN, Germany) according to the manufacturer's protocol. The presence of HPV-DNA was investigated using the MY09 / MY11 primers by the Polymerase Chain Reaction (PCR) method, positive samples were amplified using type-specific primers by PCR method and HPV typing was performed. HPV-DNA positivity was detected as 6% (3/50) in the study. Two samples were typed as HPV16; and one samples was typed as HPV31. It was observed that all HPV DNA positive samples were high risk oncogenic HPV types. When the probable risk factors are examined; It was observed that the first sexual intercourse age of patients was 16-21 years, and the number of pregnancies was ≥3 among the HPV-DNA positive women. A statistically significant relation was found with HPV-DNA positivity between the age of first sexual intercourse and the number of pregnancies (p

Introduction: Coronaviruses are the agents of viral respiratory infections and cause severe respiratory infections, especially in the elderly, those with chronic disease and immunocompromised patients. The aim of this study was to determine the positive and common types of Coronaviridae family in patients admitted to our hospital in the four-year period before the COVID 19 pandemic (2016-2020) and to investigate the distribution of coronavirus positivity by age groups, months, seasons and years. Materials and Methods: Between February 2016 and January 2020, clinical samples of 1164 female (45%) and 1428 (55%) male patients were sent to the molecular virology laboratory from the various clinics of Gazi University, Faculty of Medicine Hospital due to symptoms of acute respiratory tract infection. Coronaviridae family positivity was investigated retrospectively in clinical samples of 2592 patients aged 0-101 years. Nucleic acid extraction from the clinical samples was performed with the ‘EZ1 Virus Mini Kit’. For viral DNA amplification, it was performed by multiplex Real-Time PCR method using ‘FTD Respiratory Pathogen 21’ test. Statistical analysis of the distribution of coronavirus positivity by age groups, months, seasons and years was done by SPSS 20.0 computer program. Results: Two hundred and twenty-nine (8.8%) of the clinical samples were found to be positive for any Coronavirus type. The most common type of Coronavirus was found to be CoV-229E with 52% (119/229). The distribution of other coronavirus types including CoV-HKU1, CoV-OC43 and CoV-NL63 was determined as 19.2% (44/229), 17.4% (40/229) and 14% (32/229) respectively, and the most common type of Coronavirus changed from year to year. Single Coronavirus positivity was found to be 48.1%, its association with other viruses was 51.9%. The highest coinfection of Coronavirus was found in Rhinovirus (35.3%) and influenza A virus (19.3%). Patients over 60 years of age were found to have a higher rate (30.6%) positivity compared to other age groups (p< 0.05). The highest rate of Coronavirus positivity was observed in January (17.4%) and the lowest rate in June (1.7%). It was observed that the highest rate of positivity (44.2%) was in winter and the lowest rate (8.2%) was in summer (p< 0.05). Coronaviruses were found to be detected at higher rates in winter with seasonal variation (p< 0.05). Conclusion: Since it is not possible to diagnose viral respiratory tract infections based on clinical findings, viral respiratory panel and Multiplex real time PCR test is a fast and useful method in routine diagnosis for early diagnosis and treatment and to prevent unnecessary use of antibiotics. Coronaviridae family positivity is seen in patients over 60 years of age and in seasonal variation, with higher rates in winter.

Introduction: Coronaviruses are the agents of viral respiratory infections and cause severe respiratory infections, especially in the elderly, those with chronic disease and immunocompromised patients. The aim of this study was to determine the positive and common types of Coronaviridae family in patients admitted to our hospital in the four-year period before the COVID-19 pandemic (2016-2020) and to investigate the distribution of coronavirus positivity by age groups, months, seasons and years. Materials and Methods: Between February 2016 and January 2020, clinical samples of 1164 female (45%) and 1428 (55%) male patients were sent to the molecular virology laboratory from the various clinics of Gazi University, Faculty of Medicine Hospital due to symptoms of acute respiratory tract infection. Coronaviridae family positivity was investigated retrospectively in clinical samples of 2592 patients aged 0-101 years. Nucleic acid extraction from the clinical samples was performed with the ‘EZ1 Virus Mini Kit’. For viral DNA amplification, it was performed by multiplex Real-Time PCR method using ‘FTD Respiratory Pathogen 21’ test. Statistical analysis of the distribution of coronavirus positivity by age groups, months, seasons and years was done by SPSS 20.0 computer program. Results: Two hundred and twenty-nine (8.8%) of the clinical samples were found to be positive for any Coronavirus type. The most common type of Coronavirus was found to be CoV-229E with 52% (119/229). The distribution of other coronavirus types including CoV-HKU1, CoV-OC43 and CoV NL63 was determined as 19.2% (44/229), 17.4% (40/229) and 14% (32/229) respectively, and the most common type of Coronavirus changed from year to year. Single Coronavirus positivity was found to be 48.1%, its association with other viruses was 51.9%. The highest coinfection of Coronavirus was found in Rhinovirus (35.3%) and influenza A virus (19.3%). Patients over 60 years of age were found to have a higher rate (30.6%) positivity compared to other age groups (p< 0.05). The highest rate of Coronavirus positivity was observed in January (17.4%) and the lowest rate in June (1.7%). It was observed that the highest rate of positivity (44.2%) was in winter and the lowest rate (8.2%) was in summer (p< 0.05). Coronaviruses were found to be detected at higher rates in winter with seasonal variation (p< 0.05). Conclusion: Since it is not possible to diagnose viral respiratory tract infections based on clinical findings, viral respiratory panel and Multiplex real time PCR test is a fast and useful method in routine diagnosis for early diagnosis and treatment and to prevent unnecessary use of antibiotics. Coronaviridae family positivity is seen in patients over 60 years of age and in seasonal variation, with higher rates in winter.

Giriş: Rotavirüs (RV), çocukluk çağında görülen gastroenteritlerin ve özellikle gelişmekte olan ülkelerde gastroenterite bağlı mortalite vemorbiditenin en yaygın nedenlerindendir. Bu çalışmanın amacı, hastaneye başvuran, 0-65 yaş arasında, akut gastroenteritli, RV hızlıantijen testi pozitif hastaların dışkı örneklerinde RV’ün genotiplerinin RT-PCR yöntemi ile belirlenmesidir.Materyal ve Metod: Bu çalışma Gazi Üniversitesi Tıp Fakültesi Mikrobiyoloji Anabilim Dalı’na Ocak 2013 ile Nisan 2018 tarihleri arasındagastroenterit şikayeti ile başvuran ve dışkıları Mikrobiyoloji laboratuvarına yollanan ve immünokromatografik yöntem ile pozitifbulunan, 0-65 yaş arasındaki 87 (40 kız, 47 erkek) hastanın dışkı örnekleri toplanarak çalışılmıştır. RV VP-7 amplifikasyonu Beg9 ve End9primerleri kullanılarak, G tiplendirme G1-G4 ve G9 için özgül primerler kullanılarak çalışılmıştır; VP-4 amplifikasyonu con-2 ve con-3 primerlerikullanılarak, P tipleri; P[8], P[4], P[6] ve P[9] için özgül primerler ile belirlenmiştir. VP4 ve VP7 gen amplifikasyonu için AccessQuickRT-PCR (Promega Corporation, Madison, WI), genotiplendirme için de PCR Mastermix (Promega, Madison, WI) kullanılmıştır.Bulgular: RV antijen pozitifliği saptanan olgularda cinsiyetler arasında istatistiksel olarak anlamlı bir fark saptanmamıştır. RV infeksiyonuen sık 12-23 aylık çocuklarda saptanmıştır. Antijen pozitifliğinin en sık kış ve sonbahar mevsiminde yoğunlaştığı izlenmiştir.Tiplendirme sonucunda G1 (%25.80), G2 (%3.22), G3 (%4.30), G4 (%6.45), G9 (%60.21) G tipi olarak belirlenmiştir. P4 (%1.14),P8 (%93.10), P6 (%5.74) P tipi olarak belirlenmiştir. Hem G hem de P tipleri birlikte tespit edilmiştir. En sık görülen G/P kombinasyonuG9P[8] (%56.98) ve G1P[8] (%22.58) olduğu saptanmıştır.Sonuç: Tüm dünyada olduğu gibi Ankara’daki RV infeksiyonu olan olgularda da G9 ve P[8]’in sık saptanan genotipler olduğu görülmüştür.Türkiye’de yapılan çeşitli çalışmalara benzer şekilde en sık G9P[8] tespit edilmiştir. Bu nedenle bu veriler, RV aşı stratejilerindegöz önünde bulundurulmalıdır.

Objective: The aim of this study was to retrospectively investigate the presence of Parvovirüs B19-DNA in pregnant women diagnosed with fetal anomaly and hydrops fetalis and its association with fetal infection and viral load. Method: Twelve clinical samples of eleven patients referred to our laboratory between July 2014-March 2018 were included in the study. Parvovirüs B19-IgM and IgG antibodies and were evaluated by ELISA (NovaTec, Germany) and the presence of Parvovirus-B19 DNA was quantatively investigated by Real-Time PCR (LightMix® Kit Parvovirus B19, Roche, Germany). Results: Parvovirus-B19 DNA-positivity was identified in 2 of 12 (16.7%) samples. Parvovirus-B19 DNA was detected in both amniotic fluid and serum samples, which were simultaneously taken from 22-week pregnant women with fetal anomalies with 106 copies/ml and with 10³ copies/ml, respectively. Parvovirus-B19 was detected as IgM negative in serological analysis. When IgG was negative, serological test for IgM was recommended to be repeated 2-4 weeks later, and a miscarriage occurred in the 8th gestational week of a woman whose IgM was evaluated as being in “grey zone”. Chromosome analysis of one of the patients, whom ParvovirusB19 DNA was detected, was considered normal and a healthy baby was born. Pregnancy was terminated in three other pregnants included in the study due to the presence of fetal anomalies. The pregnancies were terminated due to the diagnosis of hydrops fetalis in 2, and fetal distress in 2, fetal hydrothorax in 1 patient, while two patients had term deliveries. Conclusion: Even if the results of serological analysis were negative, Parvovirus B19-DNA can be quantitatively detected up to 10 copies/ml by Real-Time-PCR. It should not be forgotten that detection of the presence and viral load of Parvovirus B19-DNA by Real-Time PCR is quite important in terms of early diagnosis of fetal Parvovirus B19 infection in pregnancies.

Introduction: 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® 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.

Background Parvoviruses are small DNA viruses causing erythema infectiosum, which is known as the fifth disease. The aim of this study was to investigate the presence of Parvovirus B19 DNA by Real-Time-PCR retrospectively in clinical samples of children diagnosed as acute leukemia and aplastic anemia when investigating the cause of pancytopenia and to investigate its relationship with the clinical manifestations. Methods The study samples were collected between March 2014 and March 2018 in Gazi University, Faculty of Medicine, Department of Pediatric Hematology. Sixty pediatric patients; 37 males and 23 females, were included in the study. Nucleic acid isolation was performed by using MagNA-Pure Compact Nucleic Acid Isolation Kit (Roche, Germany). Extracted DNA was studied with LightCycler® 2.0 using the Real-Time PCR method and LightCycler® Parvovirus B19 Quantification Kit (Roche, Germany), and the results were evaluated quantitatively. Parvovirus B19 DNA detection interval of the kit was 101 - 106 copies/mL. Results Sixty serum samples were investigated and 8.3% (5/60) Parvovirus B19 DNA positivity was determined. Of the five patients with Parvovirus B19 DNA positivity, three had acute lymphoblastic leukemia and two were diagnosed as aplastic anemia. Regarding viral load; 2/5, 1/5, 1/5, and 1/5 of the samples had a viral load of 102, 103, 104, and 105 copies/mL, respectively. Parvovirus B19 DNA positivity was detected in samples from March (2/5), April (2/5), and August (1/5). Conclusions Patients with acute leukemia and aplastic anemia in childhood using immunosuppressive drugs, blood, and blood products during chemotherapy, encounter Parvovirus B19 infections in the follow-up period and are diagnosed by serological and molecular methods. As a result of the study, we suggest that the detection of Parvovirus B19 DNA by Real-Time PCR method in children being admitted with pancytopenia and diagnosed as acute leukemia and aplastic anemia is useful in the follow-up and treatment.

Background/aim: To determine the frequency, genotype distribution, and genetic relatedness of adenoviruses in children under 5 years old with diarrhoea and to investigate their distribution according to clinical findings, age, months, and seasons. Materials and methods: Stool samples were collected from 180 children with acute gastroenteritis who presented from July 2007 through June 2011 at the Ankara Training and Education Hospital. Stool samples were analysed by immune chromatographic test (ICT), enzyme immunoassay (EIA), and polymerase chain reaction (PCR). All adenovirus types were determined by nucleotide sequence analysis. A phylogenetic tree was constructed by Mega 6.0 using the neighbour-joining method. Results: Five percent of the samples were positive for adenovirus (9/180) by ICT, 6.1% (11/180) by EIA, and 13.9% (25/180) by PCR. Adenovirus gastroenteritis did not show any differences in age group, sex, month, or season. In this study, 16 (64%) of the PCR positive samples were AdV41, 6 (24%) were AdV40, 2 (8%) were AdV31, and 1 (4%) was AdV7, as determined by nucleotide sequencing. Conclusion: AdV31 and AdV7 were associated with gastroenteritis. Adenovirus serotypes showed a similarity of 80% (20/25) and 20% (5/25) with Asian and American serotypes, respectively.

Introduction: The aim of this retrospective study is to investigate the relationship between clinic and presence of Epstein-Barr virus (EBV) DNA and viral load by real-time polymerase chain reaction (PCR) in patients with high risk.Methods: A total of 168 samples obtained from 160 patients, hospitalized in Gazi University Hospital between March 2014 and May 2015, were included in the study. EBV antibodies were investigated by ELISA (Dia.Pro, Milano, Italy) in clinical samples of patients, and serological profiles of patients were determined. Nucleic acid isolation was performed by High Pure Viral Nucleic Acid Kit (Roche, Germany). Isolated DNAs were amplified by LightCycler® EBV Quantitative Kit (Roche, Germany) in LightCycler 2.0 (Roche, Germany) device, and results were evaluated quantitatively.Results: EBV DNA was positive for 4.2% (7/168) of the samples. The distributions of positive rates were 14.2% (1/7) for oncology, 12.5% (1/8) for intensive care units, 4.8% (4/42) for pediatric gastroenterology, and 4.1% (1/24) for pediatric hematology. Three of the patients that EBV DNA detected had liver transplant, one had non-Hodgkin’s lymphoma, one had Burkitt’s lymphoma, one had acute renal failure, and one had gingivostomatitis and pharyngotonsillitis while follow-up. In 6/7 of the samples, EBV DNA detected 104 copies/ml, and 1/7 of the samples 105 copies/ ml. The patient whose EBV DNA load was 105 copies/ml had Burkitt’s lymphoma. EBV DNA and viral capsid antigen IgM positive were detected simultaneously only in one patient (17%).Conclusion: Early diagnosis by real-time PCR is of great importance in terms of follow-up of patients by monitoring DNA amounts and prognosis. Therefore, in immunosuppressive patients who have high levels of EBV DNA, Burkitt’s lymphoma disease should be considered.