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Öğe Emerging Technologies for the Diagnosis of Viral Infections and SARS-CoV-2(Gazi Univ, Fac Med, 2020) Altindis, Mustafa; Feyzioglu, BahadirCoronavirus disease 2019 (COVID-19) is a newly emerging infection caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Based on the rapid increase in the rate of human infection, the World Health Organization (WHO) has classified the COVID-19 outbreak as a pandemic. Considering that there is no specific drug or vaccine yet for COVID-19, effective rapid diagnosis of viruses has become very important in terms of early detection and control of the outbreak. The routine difficulties of isolating the virus necessitated the diagnosis to be made with more serological tests for many years. However, in recent years, molecular tests that provide fast and high-quality viral diagnosis information have started to take their place in laboratories. Syndrome-based PCR tests after PCR and multiplex PCR tests are also approaches that question the direct factor and accelerate the diagnosis and treatment. LAMP PCR technology has also developed rapidly, and the diagnosis time has been shortened in the field or at the bedside with very small portable devices. As a new technology, CRISPR diagnostic methods and portable DNA sequencing devices will be very useful in the diagnosis of viral infections in the clinic for rapid results per patient. With immunoprecipitation systems using luciferase-labeled antigens, virus identification, quantitation, antiviral efficacy can be monitored. COVID-19 outbreak management increased the need for very fast and reliable tests and triggered the laboratory biotechnology industry. The entire world is experiencing a dynamic pandemic process in which the benefits of new, highly sensitive, accessible and portable identification methods will be tested. The presence of a large number of applications in the approval process for these methods provides strong evidence that SARS-CoV-2 diagnostic algorithms will have richer and productive solutions in the near future. Experiences will be guiding in better understanding of other viral infections, establishing bedside diagnostic solutions, providing more effective treatments.Öğe Emerging Technologies for the Diagnosis of Viral Infections and SARS-CoV-2(Gazi Univ, Fac Med, 2020) Altindis, Mustafa; Feyzioglu, BahadirCoronavirus disease 2019 (COVID-19) is a newly emerging infection caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Based on the rapid increase in the rate of human infection, the World Health Organization (WHO) has classified the COVID-19 outbreak as a pandemic. Considering that there is no specific drug or vaccine yet for COVID-19, effective rapid diagnosis of viruses has become very important in terms of early detection and control of the outbreak. The routine difficulties of isolating the virus necessitated the diagnosis to be made with more serological tests for many years. However, in recent years, molecular tests that provide fast and high-quality viral diagnosis information have started to take their place in laboratories. Syndrome-based PCR tests after PCR and multiplex PCR tests are also approaches that question the direct factor and accelerate the diagnosis and treatment. LAMP PCR technology has also developed rapidly, and the diagnosis time has been shortened in the field or at the bedside with very small portable devices. As a new technology, CRISPR diagnostic methods and portable DNA sequencing devices will be very useful in the diagnosis of viral infections in the clinic for rapid results per patient. With immunoprecipitation systems using luciferase-labeled antigens, virus identification, quantitation, antiviral efficacy can be monitored. COVID-19 outbreak management increased the need for very fast and reliable tests and triggered the laboratory biotechnology industry. The entire world is experiencing a dynamic pandemic process in which the benefits of new, highly sensitive, accessible and portable identification methods will be tested. The presence of a large number of applications in the approval process for these methods provides strong evidence that SARS-CoV-2 diagnostic algorithms will have richer and productive solutions in the near future. Experiences will be guiding in better understanding of other viral infections, establishing bedside diagnostic solutions, providing more effective treatments.Öğe Hepatitis B Virus Carrying Drug-resistance Compensatory Mutations in Chronically Infected Treatment-naive Patients(Galenos Yayincilik, 2016) Altindis, Mustafa; Aslan, Ferhat Gurkan; Koroglu, Mehmet; Eren, Ayla; Demir, Leyla; Uslan, Mustafa Ihsan; Aslan, SavasObjective: The prevalence of hepatitis B virus (HBV) is highly variable throughout the world. Geographical regions are classified according to the prevalence of hepatitis B surface antigen in the general population as high (>8%), moderate (2-7%), and low endemicity (<2%). Turkey has a moderate endemicity level of HBV infection which is a serious health problem. Currently, there are various nucleos(t)ide analogues with anti-HBV activity and they are mostly used in the treatment of chronic hepatitis B (CHB) and cirrhosis. The risk of drug resistance increases because these drugs are still being used as monotherapy. It has been reported that HBV drug resistance-related mutations can occur also in patients who are classified as treatment-naive and who have not received any oral anti-HBV treatment. Materials and Methods: This prospective and descriptive epidemiological study aimed to determine the genotype/subgenotypes of HBV and to investigate the drug resistance mutations in treatment-naive CHB patients. The study included 149 CHB patients who had no chronic co-infections, and have not received treatment for CHB infection. In 53 of the samples collected from the patients, the amount of viral DNA was enough for sequence analysis to search for drug resistance. BigDyeTM Terminator Cycle Sequencing Kit (Applied Biosystems, Foster City, Calif., USA) was used for sequencing of the serum samples from these patients and drug resistance mutations were determined and genotype/subgenotype detection was performed. Results: The mean viral load value was calculated as 9.84x10(6), and there was no primary drug resistance in any of these 53 samples which were sequenced. There were compensatory resistance-related amino acid changes in 19 samples. Genotype D was determined as HBV in all cases. Conclusion: The early detection of drug resistance-related mutations can be important in determination of treatment protocol, and prevention of unnecessary drug use, complications, and economic loses.Öğe A Multicenter Evaluation of Blood Culture Practices, Contamination Rates, and the Distribution of Causative Bacteria(Briefland, 2016) Altindis, Mustafa; Koroglu, Mehmet; Demiray, Tayfur; Dal, Tuba; Ozdemir, Mehmet; Sengil, Ahmet Zeki; Atasoy, Ali RizaBackground: The prognostic value of blood culture testing in the diagnosis of bacteremia is limited by contamination. Objectives: In this multicenter study, the aim was to evaluate the contamination rates of blood cultures as well as the parameters that affect the culture results. Materials and Methods: Sample collection practices and culture data obtained from 16 university/research hospitals were retrospectively evaluated. A total of 214,340 blood samples from 43,254 patients admitted to the centers in 2013 were included in this study. The blood culture results were evaluated based on the three phases of laboratory testing: the pre-analytic, the analytic, and the post-analytic phase. Results: Blood samples were obtained from the patients through either the peripheral venous route (64%) or an intravascular catheter (36%). Povidone-iodine (60%) or alcohol (40%) was applied to disinfect the skin. Of the 16 centers, 62.5% have no dedicated phlebotomy team, 68.7% employed a blood culture system, 86.7% conducted additional studies with pediatric bottles, and 43.7% with anaerobic bottles. One center maintained a blood culture quality control study. The average growth rate in the bottles of blood cultures during the defined period (1259 -26,400/year) was 32.3%. Of the growing microorganisms, 67% were causative agents, while 33% were contaminants. The contamination rates of the centers ranged from 1% to 17%. The average growth time for the causative bacteria was 21.4 hours, while it was 36.3 hours for the contaminant bacteria. The most commonly isolated pathogens were Escherichia coli (22.45%) and coagulase-negative staphylococci (CoNS) (20.11%). Further, the most frequently identified contaminant bacteria were CoNS (44.04%). Conclusions: The high contamination rates were remarkable in this study. We suggest that the hospitals' staff should be better trained in blood sample collection and processing. Sterile glove usage, alcohol usage for disinfection, the presence of a phlebotomy team, and quality control studies may all contribute to decreasing the contamination rates. Health policy makers should therefore provide the necessary financial support to obtain the required materials and equipment.Öğe The Prevalence of Mixed Genotype Infections in Turkish Patients with Hepatitis C: a Multicentered Assessment(Clin Lab Publ, 2019) Kulah, Canan; Altindis, Mustafa; Akyar, Isin; Gokahmetoglu, Selma; Sayiner, Arzu; Kaleli, Ilknur; Fidan, IsilBackground: HCV virus infections are one of the major health problems in the world that can cause cirrhosis and liver cancer at a higher rate than other hepatitis data. The aim of this study was to determine the prevalence of mixed infections with different HCV genotypes in Turkey and also to evaluate the current HCV genot pe and subtype distributions by a multicentered assessment. Methods: The HCV genotype data of 17,578 hepatitis C patients collected from 23 centers from different geographic regions covering all Turkey were collected. The data included information about the HCV genotypes in the last 10 years (bail een 2007 and 2016), demographic properties of the patients and the methods/systems used to determine the genotypes. Results: Two hundred twenty-eight of the patients (1.3%) had mixed genotype. The most common mixed genotype combination was 1b + 4 (0.83%) followed by 1a + 1b (0.26%). Genotype distribution varies according to geographical regions. However, genotype 1 (82.92%) was the most common genotype in all regions and all years. This was followed by genotype 3 (7.07%) and genotype 4 (5.43%). A variety of methods were used by the centers including sequencing, pyrosequencing, real-time PCR, in-house RFLP, reverse hybridization (LIPA), and hybridization. Conclusions: Infection with mixed HCV genotypes in Turkey is uncommon. Genotype distribution varies according to geographic regions; the most common genotype 1 is encountered all oN er the country, while genotypes 3 and 4 are only in some of the centers. Since there is limited information about mixed HCV infection, further investigations are needed to determine the clinical importance of mixed HCV infection.Öğe Six-year distribution pattern of hepatitis C virus in Turkey: a multicentre study(Taylor & Francis Ltd, 2016) Altindis, Mustafa; Dal, Tuba; Akyar, Isin; Karatuna, Onur; Gokahmetoglu, Selma; Ulger, Seda Tezcan; Kulah, CananHepatitis C infection is a public health problem. The aim of this retrospective study was to determine the distribution of hepatitis C virus (HCV) genotypes in seven regions of Turkey, by evaluating 7002 patients with chronic HCV in a six-year period. During the 2009-2014 period, serum/plasma samples from 7002 new consecutive HCV RNA positive patients were collected. The female patients were 3867 (55.2%). The genotype distribution of HCV patiens was evaluated by ages and years. Statistical analysis was performed by using the Mann-Whitney test and the chi(2) analysis. During the six-year period, genotype 1b was the most common genotype (67.7%) followed by untypeable genotype 1 (7.7%), genotype 4 (7.3%) and genotype 3 (6.7%). In 2014, genotype 3 was the second most common one (11.3%) and genotype 4 was the third most common one (9.8%). In the group with <25 years old patients, genotype 1b was most common (78.48%, 62/79) between the years of 2009 and 2011, whereas genotype 3 (34.8%, 86/247), between the years of 2012 and 2014. Genotype 1b was the most common in the groups between 26 and 35 years, 36 and 45 years, 46 and 55 years, 56 and 65 years. The rate of genotype 3 was increased from 4.78% to 10.06% and the rate of genotype 4 was increased from 1.3% to 3.84%, from 2009-2011 to 2012-2014. In recent years, genotypes 3 and 4 have gained importance. New therapeutic strategies and survey studies may be required for the modified HCV genotype pattern.