Browsing by Author "Akçali S."

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    Effects of Different Disinfectants on Decontamination of Laryngoscopes; [Laringoskoplarin Dezenfeksiyonunda Kullanilan Dezenfektanlarin Etkinliǧinin Karşilaştirilmasi]
    (2003) Tekin I.; Arican I.; Akçali S.; Şanlidaǧ T.; Özbakkaloǧlu B.
    Guidelines for controlling possible contamination of laryngoscopes should be formulated with the benefit of relevant experimental data. In this study, the effects of five different disinfectants commonly used for the disinfection of laryngoscopes are evaluated. We formed 14 groups consisting of 10 blades in each. The first 7 groups were contaminated with hospital related meticillin resistant Staphylococcus aureus (MRSA), and the other 7 groups with hospital related multiple resistant Pseudomonas aeruginosa (PA). For the first group of blades, no disinfection procedure was carried out and, were assumed as a control group. Blades in other groups were rested for 10 minutes in containers containing 70 % alcohol, 1/100 dilution of cetrimide, 1/100 dilution of chlorhexidine, 1/10 dilution of chlorhexidine, 1/10 dilution of povidone iodine, and 1/100 dilution of ammonium chloride in groups II,III,IV,V,VI, and VII respectively. Disinfectant used in a group was considered as effective when growth was seen in 5 or less than 5 plates representing that group. All disinfectants tested were found effective on decontamination of laryngoscopes. 5 different moderate level disinfectants which are commonly used for the disinfection of laryngoscopes have been found effective even on resistant hospital microorganisms like MRSA and P. aeruginosa. Finding effective, cheap and time saving methods by choosing a specific disinfectant, concentration and contact time is not difficult as long as clinicians are aware of the principles of the laringoscopes disinfection procedures.
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    Clinical significance of TT virus infection in children with chronic hepatitis B
    (2005) Kasirga E.; Sanlidag T.; Akçali S.; Keskin S.; Aktas E.; Karakoç Z.; Helvaci M.; Sözen G.; Kuzu M.
    Background: The pathogenic role of TT virus (TTV) is not clear in patients with chronic hepatitis B. The aims of the present study were to determine the frequency of TTV positivity in serum and saliva samples and the possible role of TTV in children with chronic hepatitis B. Methods: Sera and saliva from 29 healthy children and 25 children with chronic hepatitis B were tested for TTV-DNA by means of real-time polymerase chain reaction (PCR). Results: Fifty-two percent (13/25) of the serum samples and 32% (8/25) of the saliva samples were positive for TTV-DNA in children with chronic hepatitis B. In healthy non-transfused children, TTV-DNA was detected in 58% (17/29) of the serum samples and 41% (12/29) of the saliva samples. Six (46%) of 13 children with chronic hepatitis and 10 (59%) of 17 healthy children had TTV-DNA positivity both in serum and saliva samples. Two serum samples were negative for TTV-DNA while the saliva samples were positive for TTV-DNA in chronic hepatitis B and control groups. Mean age, sex, serum alanine aminotransferase levels, hepatitis B virus (HBV)-DNA values were similar in TTV-positive and -negative children with chronic hepatitis B. However, total histologic activity index (HAI), periportal necrosis and portal inflammation scores were significantly higher in children with HBV-DNA and TTV-DNA viremia (P = 0.013, P = 0.008, P = 0.015, respectively). Conclusions: Because total HAI, periportal necrosis and portal inflammation scores were higher in children with TTV coinfection, TTV infection may contribute to the progression of liver damage in children with chronic hepatitis B.
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    Comparison of interferon-gamma whole blood assay with tuberculin skin test for the diagnosis of tuberculosis infection in tuberculosis contacts; [Temaslιlarda tüberküloz enfeksiyonunun tanιsι için interferon-gama tam kan testi ile tüberkülin deri testinin karşιlaştιrιlmasι]
    (2007) Öztürk N.; Sürücüoǧlu S.; Özkütük N.; Gazi H.; Akçali S.; Köroǧlu G.; Çiçek C.
    Tuberculin skin test which is used for the detection of latent tuberculosis (TB), has many disadvantages such as false positivities due to cross reactions between environmental mycobacteria and BCG strain, false negativities due to immunosuppression and malpractice, and also difficulties in application and evaluation. Recently a new diagnostic test which measures the production of interferon (IFN)-gamma in whole blood upon stimulation with specific ESAT-6 and CFP-10 antigens of Mycobacterium tuberculosis has been introduced. Since most of the mycobacteria other than tuberculosis and BCG strain do not contain these antigens, the detection of IFN-gamma levels indicates the specific T-cell response against M.tuberculosis. The aim of the study was to compare the tuberculin skin test and whole blood IFN-gamma assay (QuantiFERON®-TB Gold, Cellestis Ltd, Carnegie, Victoria, Australia) for the identification of latent TB infection in the contacts with active TB patients. The tests results were evaluated by using Kappa (K) analysis, and K coefficients of <0.4, 0.4-0.75 and >0.75 were accepted as poor, moderate and excellent agreements, respectively. A total of 233 subjects from three risk groups were included to the study. Group 1 included the household members (n=133) who had contact with smear positive index cases, Group 2 included the subjects from community (n=46) who had contact with smear positive index cases, and Group 3 included health care workers (n=74) who had contact with TB patients or their specimens. The positivity rates of tuberculin skin test and IFN-gamma assay in the cases were found as 37% and 42%, respectively. There were no significant differences among the three patient groups with regard to the results of the tuberculin skin test (p>0.05). However, the positive result of the IFN-gamma assay in Group 1 was found statistically higher than the other groups (51.3%, p=0.013). A poor agreement between the two tests was detected in the results taken from 233 subjects (65.7%, K=0.28), while agreement was moderate in unvaccinated group (72.7%, K=0.44). Evaluation of agreement rates of the tests according to the risk groups yielded 64.6% (K=0.3) for Group 1, 71.7% (K=0.32) for Group 2, and 63.5% (K=0.21) for Group 3, which all coefficients showed poor agreement. Although IFN-gamma blood assay has many advantages such as objective and quantitative results, no interference with vaccination due to the use of specific antigens and being practical, the high cost and the need for well-equipped laboratory are its disadvantages. As a result it was concluded that, IFN-gamma blood assay has limited value for the detection of latent TB infection in our country, since the prevalence of TB infection and BCG vaccination rates are high in Turkey.
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    Common viral etiologies of community acquired lower respiratory tract infections in young children and their relationship with long term complications; [Küçük çocuklarda toplum kökenli viral alt solunum yolu enfeksiyonu etkenlerinin sιklιǧι ve uzun dönem komplikasyonu ile ilişkileri]
    (2008) Yüksel H.; Yilmaz Ö.; Akçali S.; Söǧüt A.; Yilmaz Çiftdoǧan D.; Urk V.; Ertan P.; Şanlidaǧ T.
    Viral lower respiratory tract infections (LRTIs) and their late complications are important causes of morbidity and mortality in childhood. The aims of this study were the detection of viral agents that cause community-acquired LRTIs in young children and investigation of the relationship between viral etiology and bronchiolitis obliterans (BO) which is one of the late complications of LRTIs. A total of 151 children (86 male, 65 female; mean age: 2.9 ± 1.9 years) who were diagnosed to have LRTIs between the period of 2002-2004, at Pediatric Allergy and Pulmonology Department of a University Hospital in Manisa (located in the Aegean region of Turkey) were included to the study. The presence of respiratory viruses [respiratory syncytial virus (RSV), influenza virus type A and B, parainfluenza virus types 1, 2 and 3, adenovirus] in the nasopharyngeal aspirate specimens collected from children have been searched by direct fluorescence antibody test (Biotrin, Ireland). Respiratory viruses were detected in 25.2% (38/151) of the patients with LRTIs, while this rate was 46.8% (22/47) for 2002 period, 13.3% (8/60) for 2003 period and 18.2% (8/44) for 2004 period. RSV and adenoviruses both detected with a frequency of 31.5% (n= 12/38); were the most common agents encountered, and followed by parainfluenza (10/38, 26.3%) and influenza (9/38, 23.6%) viruses. Postinfectious BO have been diagnosed in 7.3% (11/151) of the patients; seven in 2002, one in 2003 and three in 2004 periods. Viral etiology were present in all of the patients who developed BO in 2002, while viral infection was detected in one of the patients who developed BO in 2003-2004 periods. Adenoviruses were the most frequently detected agents (n= 5) in BO cases with viral etology (n= 8). Viral agents were found positive in 72.7% (8/ 11) and 21.4% (30/140) of the patients with and without BO development, respectively, and this difference was found statistically significant (p= 0.02). Besides, BO development was detected in 21.1% (8/38) and 2.6% (3/113) of LRTI patients with and without viral etiology, respectively, and this difference was also significant (p< 0.05). In conclusion, the long term follow-up is important in young children with viral LRTIS for the early diagnosis of complications. Thus the identification of viruses might aid in estimation of prognosis.
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    Distribution of hepatitis C virus genotypes in Manlsa region, Turkey; [Manisa bölgesinde hepatit C virus genotiplerinin daǧilimi]
    (2009) Şanlidaǧ T.; Akçali S.; Özbakkaloǧlu B.; Ertekin D.; Akduman E.
    The duration of hepatitis C virus (HCV) infection and the response to the standard therapy is strongly related to the HCV genotypes. In addition, the geographical distribution of HCV genotypes is important for the epidemiological studies in terms of distribution and possible risk groups. The aim of this retrospective study was to investigate the distribution of HCV genotypes in Manisa region (located at the Aegean part of Turkey). A total of 100 anti-HCV (microparticle EIA; Abbott Laboratories, USA) and HCV-RNA (real time RT-PCR; Applied Biosystems, USA) positive patients (53 female, 47 male; mean age: 44.4 ± 10.4 years), who were admitted to Celal Bayar University Medical School Hospital between 2002-2005, were included to the study. Quantitative HCV-RNA levels of the patients were between 10 4-10 8 copies/ml. Complementary DNAs obtained from HCV-RNAs isolated by Invitek RTP DNA/RNA Virus Mini Kit were used for genotyping with selected primers [primer 11 (5'-AGG TCT CTG AGA CCG TGC ACC ATG AGC AC-3') and primer 13 (5'-CTG TGA GGA ACT ACT GTC TT-3') for the first PCR; primer 12 (5'-ACT GCC TGA TAG GGT GCT TGC GAG TG-3') and primer 14 (5'-CAC GCA GAA AGC GTC TAG-3') for the second PCR]. The RT-PCR products were purified with Invisorb Spin PCRapid Kit and sequenced by BigDye Terminator v3.1 Cycle Sequencing Kit in ABI Prism 310 Genetic Analyzer. Genotype 1 was found in 92% of the patients (92%) and genotypes 2 and 4 were found in 7% of the patients, while HCV genotype could not be identified in one patient (1%). When evaluating the subtypes, genotype 1 b was determined in 90 patients (90%), genotype 4a in five patients (5%), genotype 1 a in two patients (2%) and genotype 2a in two patients (2%). In conclusion, 1 b was found to be the most common HCV genotype in Manisa region in concordance with the previous data obtained in Turkey, followed by genotype 4a, although a rare one. The data of this study is noteworthy especially for the arrangement of treatment and follow-up of HCV infected patients.
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    Seroprevalance of chlamydophila pneumoniae in patients with alzheimer's disease and vascular dementia; [Alzheimer ve vasküler demanslı hastalarda chlamydophila pneumonaie seroprevalansı]
    (Ege University Press, 2010) Ecemiş T.; Mavioǧlu H.; Özkütük N.; Akçali S.; Karaçam M.; Şanlidaǧ T.
    In recent years, it was been argued that Chlamydophila pneumoniae, which is an intracellular pathogen capable of causing chronic infection, might be effective in some forms of dementia, an argument confirmed or rejected by some studies. The objective of this study was to determine if there was an association between C. pneumoniae infection and Alzheimer's disease and vascular dementia. We tested 54 patients with Alzheimer and 29 patients with vascular dementia and 50 controls for C. pneumoniae IgG and IgA antibodies and analyzed the results statistically. C. pneumoniae IgG antibodies were found in 25 patients (49.2%) with Alzheimer's disease, 15 patients (51.8%) with vascular dementia and 22 controls (44%) whereas 6 patients (11.1%), 2 patients (6.9%) and 3 controls (6%), respectively, tested positive for IgA. It was found no serological evidence for a significant association between C. pneumoniae and Alzheimer's disease as well as vascular dementia.
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    Molecular typing and sequencing of adenovirus isolated from a conjunctivitis outbreak in a neonatal intensive care unit by PCR
    (2012) Çiçek C.; Şanlidaǧ T.; Siyah Bilgin B.; Pullukçu H.; Akçali S.; Altun Köroǧlu O.; Yalaz M.; Kültürsay N.
    Aim: We aimed to evaluate the molecular typing of adenovirus isolated during an epidemic at the Ege University Children's Hospital neonatal intensive care unit (NICU). Materials and methods: During the NICU outbreak management, 40 clinical samples (from 15 newborn infants and 25 health care providers) were sent to a microbiology laboratory in viral transport media. All the samples were processed using a direct fluorescent antibody (DFA) test and a shell vial cell culture followed by adenovirus polymerase chain reaction (PCR) and DNA sequencing. PCR and DNA sequencing for adenovirus hexon gene hypervariable regions 1-6 were done after DNA extraction from clinical specimens. Adenovirus typing was done using BLAST analysis. Results: Ten adenoviruses were isolated from 4 out of 10 infants, 3 out of 5 hospital staff with conjunctivitis, and 3 asymptomatic staff. Ten positive samples were identified as adenovirus type 8 by using BLAST analysis. Conclusion: We isolated adenovirus type 8, one of the most common serotypes causing conjunctivitis, during an adenovirus outbreak in our NICU. The highest positivity was obtained using the PCR method. Although DFA was positive in a limited number of cases, this test was applied rapidly at the beginning of the epidemic and contributed to the prevention of further spread. © TÜBİTAK.
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    The threshold value of anti-HCV test in the diagnosis of HCV infection; [HCV Enfeksiyonu Tanısında Anti-HCV Testi ve Eşik Deǧer]
    (Turkiye Klinikleri, 2012) Ecemiş T.; Akçali S.; Erbay Dündar P.; Şanlidaǧ T.
    Objective: The initial step in the diagnosis of hepatitis C virus (HCV) infection is to screen for anti-HCV antibody, followed by confirmation of positive results with nucleic acid amplification tests. In the recent studies, using reactivity threshold, S/Co (signal to cut-off) ratio greater than 1 has yielded results that are highly consistent with HCV-RNA test. We aimed to determine the most appropriate S/Co level for anti-HCV enzyme immunoassay (EIA) that would predict HCV infection. Material and Methods: We compared the results of 387 patients acquired by Anti-HCV using microparticle EIA and HCV-RNA using hybridization methods. Taking the HCV-RNA test as gold standard for HCV infection, the sensitivity, specificity and predictive values of EIA test were determined and receiver operating characteristic (ROC) analysis was performed to detect the best threshold of reactivity. Results: EIA test showed 197 (49.2%) positive and 190 (50.9%) negative results, and the sensitivity and specificity were calculated as 94.9% and 60.4%, respectively. Positive and negative predictive values were 38.1% and 97.9%, respectively. ROC analysis revealed that the best S/Co level was 5 and, based on this value, sensitivity and specificity were 92.4% and 76.6%, respectively. Computed positive predictive value was 50.3% and negative predictive values was 97.5%. Conclusion: We investigated the best values of reactivity for anti-HCV EIA test and found S/Co ≥5. © 2012 by Türkiye Klinikleri.
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    Seroprevalance of measles, rubella, mumps, varicella, diphtheria, tetanus and hepatitis b in healthcare workers; [Saǧli{dotless}k çali{dotless}şanlari{dotless}nda ki{dotless}zami{dotless}k, ki{dotless}zami{dotless}kçi{dotless}k, kabakulak, suçiçeǧi, difteri, tetanos ve hepatit b seroprevalansi{dotless}]
    (AVES Ibrahim Kara, 2013) Ciliz N.; Gazi H.; Ecemiş T.; Şenol S.; Akçali S.; Kurutepe S.
    Objective: We aimed to determine the antibody levels of healthcare workers of Celal Bayar University Hospital against vaccinepreventable diseases such as measles, rubella, mumps, diphtheria, tetanus, varicella and hepatitis B, and encourage compliance to recommended vaccinations for non-immune staff. Methods: The antibody levels were tested by enzyme-linked immunosorbent assay (ELISA). Demographic characteristics were collected by a questionnaire, and the history of the diseases, immunization and the sharps-related injuries were queried. Results: 44% percent of 309 healthcare personnel were exposed to occupational injury at least once, and 78.3% of the injuries were needle-stick injuries. Injuries were found to be more common among doctors and nurses, and pediatric and surgical departments, respectively. Frequency of anti-HBs positivity among healthcare workers was 84.1%, while 71.5% of healthcare workers were immunized with HBV vaccine before starting to work, and the immunization status directly correlated with the level of education. In general, high seropositivity was noted for measles (99.7%), rubella (97.0%), mumps (99.7%) and varicella (99.7%), while diphtheria (60.8%) and tetanus (93.5%) antibody levels significantly decreased with age. Histories of the disease and vaccination were not reliable while verifying the immunity status. Conclusions: It is necessary to increase adherence to universal protective measures in healthcare workers and to take corrective and protective measures for sharps-related injuries. It is also essential to increase hepatitis B vaccination rates and to confirm the immune status of medical staff working in high risk departments and diphtheria and tetanus vaccinations should be repeated once every ten years.
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    Frequency of respiratory viruses in children with lower respiratory tract infection; [Alt solunum yolu enfeksiyonu olan çocuklarda solunum yolu viral etkenlerinin sıklıǧı]
    (Kare Publishing, 2013) Akçali S.; Yilmaz N.; Güler Ö.; Şanlidaǧ T.; Anil M.
    Aim: Lower respiratory tract infections (LRTI) have high morbidity rates in children. In this study, it was aimed to investigate the prevalence of respiratory viruses in children with LRTI symptoms. Material and Method: A total of 160 children who were diagnosed with LRTI between October 2009 and March 2010 were included into the study. The presence of respiratory syncytial virus (RSV) (A+B), influenza virus (A+B), parainfluenza virus (PIV) (1, 2, 3, 4), human metapneumovirus, rhinovirus and coronavirus (OC43+229E) in throat swab samples were investigated by real-time PCR The RealAccurateTM Respiratory RT PCR Kit (PathoFinder B.V., Netherlands). Results: In 67 samples (41.8%), at least one virus which could cause acute respiratory tract infection was found. Overall, RSV was the most frequently identified virus (52.2%), followed by rhinovirus (26.8%), coronavirus (5%), metapneumovirus (2.9%) and PIV 1 (1.4%). As the other viral agents, coronavirus was detected in 4 samples (5%), hMPV was detected in 2 samples (2.9%) and PIV was detected in 1 sample (1.4%). When the frequency of coinfections was evaluated, RSV- rhinovirus association was found in 4 samples, RSV-coronavirus association was found in 1 sample, rhinovirus-coronavirus association was found in 1 sample and RSV-rhinovirus- Coronavirus association was found in 1 sample. Conclusions: In 41.8% of the study group, a viral factor responsible for the clinical signs was detected. For that reason, rapid and sensitive diagnosis of viruses which lead to respiratory infections will guide the clinician for avoidance of redundant antibiotic therapy and preventing viral hospital infections.
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    Hepatitis B virus genotype E infection in Turkey: The detection of the first case; [Türkiye'de ̄lk Kez Saptanan Hepatit B Virus Genotip E Enfeksiyonu]
    (Ankara Microbiology Society, 2014) Sayan M.; Daʇ T.Ş.; Akçali S.; Arikan A.
    Hepatitis B virus (HBV) infection is a global major health problem. Currently, 10 genotypes (A-J) of hepatitis B virus (HBV) are identified based on the nucleic acid sequence heterogeneity, and these genotypes have been shown to have distinct geographic distribution. Reports of the previous studies indicated that the genotype D is the predominant type among hepatitis B patients in different regions of Turkey. However, recent studies indicated that other HBV genotypes are also seen with an increasing rate. Although epidemiological and clinical information on genotype E infection is currently limited, it is known that genotype E infection is common in West and Central Africa. In this report, the first case of HBV genotype E infection in Turkey was presented. A 22-year-old Nigerian male employee who resided in Manisa for five years was admitted to Celal Bayar University Hospital Manisa, Turkey, for his routine check-up. Since HBsAg was found positive, other HBV markers were tested with a repeated serum sample. Laboratory findings were as follows; HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc (+), anti-HCV (-), anti-HIV (-), ALT: 44 U/L and AST: 45 U/L. HBV-DNA level was detected as 700 lU/ml by real-time PCR (Artus HBV QS RGQ Qiagen, Germany). HBV-DNA isolated from the serum sample of the patient was amplified by PCR and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis and Inno-LIPA HBV genotyping method (Innogenetics, Belgium) was performed to determine multiple HBV genotype infection. On the basis of those methods the genotype of the virus was identified as genotype E. The partial sequences of the HBV polymerase gene were loaded to the international DNA data bank (GenBank) for contribution to the global HBV surveillance. This report emphasized that besides genotype D the other HBV genotypes could be found in Turkey. Since the patient was an inactive HBsAg carrier before his residence in Turkey, this case was regarded as an imported HBV genotype E case. In conclusion, detection of different HBV genotypes, their epidemiology and molecular characteristics are important for both national and global HBV surveillance and better clinical approach.
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    Miller Fisher Syndrome/pharyngeal-cervical-brachial variant of GBS overlap and human herpes Virus-6 reinfection: May there BE a relationship?; [MFS/ Faringeal-Servikal-Brakial variant GBS Çakışması ile human herpes Virüs enfeksiyonu arasında bir ilişki var mı?]
    (Ege University Press, 2016) Mavioğlu H.; Kisabay A.; Sari S.; Akçali S.; Oktan B.
    Miller Fisher Syndrome (MFS) is a rare variant of Gulliain Barre syndrome (GBS) characterized by external ophthalmoplegia, ataxia, areflexia, and usually by positive anti GQ1b antibody. It occurs through an autoimmune mechanism most frequently after Campylobacter jejuni, followed by Haemophilus influenzae infection. Although occurrence with other viruses and bacteria has been reported, the concurrence of MFS and Human Herpes Virus-6 (HHV-6) has not been reported so far. There are a few publications reporting association of GBS with HHV-6. In the present study, HHV-6 DNA with PCR was detected in the cerebrospinal fluid (CSF) of a 59 year-old female patient diagnosed with MFS/pharyngeal-cervical-brachial variant of GBS overlap from clinical findings and positive anti-GQ1b antibody in the serum. This article aims to create awareness of a possible relationship between MFS, GBS and HHV-6. © 2016, Ege University Press. All right reserved.
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    Molecular epidemiology of hepatitis b virus in northern Cyprus; [Kuzey Kibris'ta Hepatit B Virusunun Moleküler Epidemiyolojisi]
    (Ankara Microbiology Society, 2016) Arikan A.; Şanlidaǧ T.; Süer K.; Sayan M.; Akçali S.; Güler E.
    Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, C and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (< 30 lU/ml) HBV-DNA levels, so 100 samples were included in sequence analysis. Ninety-six of those cases (13 female, 87 male; mean age: 35.51 ± 12.88 years) were anti-HBc IgG, 95 were anti-HBe and five were HBeAg positive, with a mean HBV-DNA level of 5.36 x 106 ± 3.58 x 107 lU/ml. As 32 (32%) samples yielded HBV- DNA level below the threshold of 1000 lU/ml, sequence analyses were unsuccesful, eventually 68 (68/160, 42.5%) samples could be phylogenetically analyzed. The distribution of HBV genotypes/subgenotypes were found as follows: 48 were (70.6%) D/D1; four were (5.9%) D/D2; one was (1.5%) D/D3, five were (7.4%) A/A1, two were (2.9%) A/A2 and eight were (11.8%) genotype E. Among the most frequent D1 strains, 60.4% (29/48) cases were from Turkish; single D/D3 strain from Benguela (Angola) and all eight genotype E strains were from Nigerian national cases. According to the data of this first study performed in TRNC on this subject, genotype D is dominant (53/68, 78%) in Northern Cyprus and consistent with the subgenotype distribution that is similar to Turkey and mediterranean basin. The prevalences of genotype A (7/68, 10.3%) and E (8/68, 11.8%) were also remarkable. In conclusion, although Northern Cyprus is an island country the heterogeneous distribution of HBV genotype/subgenotype may be contributed to the cosmopolitan characteristics of various populations from different countries who have come here for education, work or touristic purposes.
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    Determination of drug resistance mutations of NS3 inhibitors in chronic hepatitis c patients infected with genotype; [Genotip 1 ile enfekte kronik hepatit C hastalarinda NS3 inhibitörü ilaçlarin direnç mutasyonlarinin belirlenmesi]
    (Ankara Microbiology Society, 2017) Şanlidaǧ T.; Sayan M.; Akçali S.; Kasap E.; Buran T.; Arikan A.
    Direct-Acting antiviral agents (DAA) such as NS3 protease inhibitors is the first class of drugs used for chronic hepatitis C (CHC) treatment. NS3 inhibitors (PI) with low genetic barrier have been approved to be used in the CHC genotype 1 infections, and in the treatment of compensated liver disease including cirrhosis together with pegile interferon and ribavirin. Consequently, the development of drug resistance during DAA treatment of CHC is a major problem. NS3 resistant variants can be detected before treatment as they can occumaturally. The aim of this study was to investigate new and old generation NS3 inhibitors resistance mutations before DAA treatment in hepatitis C virus (HCV) that were isolated from CHC. The present study was conducted in 2015 and included 97 naive DAA patients infected with HCV genotype 1, who were diagnosed in Manisa and Kocaeli cities of Turkey. Magnetic particle based HCV RNA extraction and than RNA detection and quantification were performed using commercial real-Time PCR assay QIASypmhony + Rotorgene Q/ArtusHCV QS-RGQ and COBAS Ampliprep/COBAS TaqMan HCV Tests. HCV NS3 viral protease genome region was amplified with PCR and mutation analysis was performed by Sanger dideoxy sequencing technique of NS3 protease codons (codon 32-185). HCV NS3 protease inhibitors; asunaprevir, boceprevir, faldaprevir, grazoprevir, pariteprevir, simeprevir and telap- revir were analysed for resistant mutations by Geno2pheno-HCV resistance tool. HCV was genotyped in all patients and 88 patients (n= 88/97, 91%) had genotype 1. Eight (n= 8/97, 8.2%) and 80 (n= 80/97, 82.4%) HCC patients were subgenotyped as 1 a and 1 b, respectively. Many aminoacid substitutions and resistance mutations were determined in 39/88 (44%) patients in the study group. Q80L, SI 22C/N, SI 38W were defined as potential substitutions (6/88 patients; 7%); R109K, R117C, S122G, 1132V, 1170V, N174S were described as potential resistance (34/88 patients; 39%); V36L, T54S, V55A, Q80H were characterized as resistance (7/88 patients; 8%) and Q80K, A156S were defined as high resistance (3/88 patients; 3%) mutations. Based on resistance and high resistance mutations, clinically significant mutations were defined in 10/88 (11%) of the patients. Our study shows that it is essential to analyse HCV NS3 protease inhibitors drug resistance before DAA treatment of CHC patients. On the other hand, our results pointed out that analysis of NS5A and NS5B genome region mutations may also be required in the near future.
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    Factors affecting side effects, seroconversion rates and antibody response after inactivated SARS-CoV-2 vaccination in healthcare workers; [Sağlık çalışanlarında İnaktif SARS-CoV-2 aşılaması sonrası yan etkiler, serokonversiyon oranları ve antikor yanıtını etkileyen faktörler]
    (Ankara Microbiology Society, 2021) Şenol Akar Ş.; Akçali S.; Özkaya Y.; Gezginci F.M.; Cengi̇Z Özyurt B.; Deniz G.; Karadağ Yalçin F.; Özer D.; Dündar Erbay P.; Eser E.
    In this study, it was aimed to prospectively evaluate the efficacy, side effects and seroconversion data of inactive severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), CoronaVac® (Sinovac, China) vaccine in healthcare workers. A total of 1053 healthcare workers who were initially seronegative (COV2T® SARS-CoV-2 Total Siemens, USA) and vaccinated with inactivated SARS-CoV-2 were included in the study. Quantitative IgG antibodies (ADVIA Centaur® SARS-CoV-2 IgG, Siemens, USA) were investigated 28 days after the first vaccine (n= 939) and the second vaccine (n= 771). In addition, neutralizing antibodies were evaluated via “enzyme linked immunosorbent assay (ELISA)” test (ACE2-RBD Neutralization Assay, Dia-Pro, Italy) 28 days after the first vaccine. Antibody response of the vaccine was evaluated statistically by univariate (Chi-square, Fisher’s exact test, Student’s t test, Mann-Whitney U, one-way ANOVA and Kruskall Wallis ANOVA tests) analysis and linear regression models. The consistency between quantitative IgG test and neutralizing antibody test was also evaluated in blood samples taken 28 days after second vaccination. Statistical analysis was determined in logarithmically transformed data with statistical analysis with SPSS 23.0 and Stata, and type 1 error level was accepted as 0.05. At least one side effect was reported by 31.3% and 26.8% of the participants after the first and second vaccine, respectively. The most frequent side effect was pain at the injection site with a frequency of 20.4% vs 21.7%. The frequency of applying to a health center due to side effects was 1.0% after the first vaccine and 0.8% after the second vaccine. The percentage of those who produced sufficient quantitative IgG was found as 25.3% (95% CI= 22.5-28.1) 28 days after the first vaccine and 97.9% (95% CI= 96.91-98.93) after the second vaccine. Neutralizing test antibody positivity was found as 97.7% 28 days after the second vaccine. In univariate analysis, the characteristics that significantly increased the quantitative IgG response against inactivated SARS-CoV-2 vaccine were young age (p< 0.01), female gender (p< 0.01), being a non-smoker (p< 0.001), not having a chronic disease (p= 0.019), having had the flu vaccine this year (p= 0.012), not being overweight or obese (p= 0.020), and having a SARS-CoV2 infection prior to vaccination (p< 0.001). In addition, allied health personnel showed significantly lower antibody responses than the other workers (p< 0.001). Multiple linear regression models revealed that, female gender, younger age, smoking and previous COVID-19 polymerase chain reaction test positivity significantly affected the quantitative IgG response after vaccination. A 99% agreement was found between the ELISA-based neutralizing antibody test and the quantitative IgG test (Kappa p= 0.783) performed on the 28th day after the second vaccination. CoronaVac® provides adequate antibody response in 25% of healthcare workers aged 18-64, after 28 days from a single vaccine, and 97% after 28 days from the second vaccine. Antibody response was significantly higher in younger ages, women, non-smokers, and those who had previously encountered SARS-CoV-2. Phase 3 and phase 4 results are needed to show effectiveness of this vaccine in real life. © 2021 Ankara Microbiology Society. All rights reserved.
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    Antibody Sustainability in SARS-CoV-2 Healthcare Professionals’ Patient Cohort; [Sağlık Çalışanları SARS-CoV-2 Hasta Kohordunda Antikor Sürdürülebilirliği]
    (Ankara Microbiology Society, 2022) Eser E.; Şenol Akar Ş.; Akçali S.; Ecemiş T.; Erbay Dündar P.; Çiçek K.; Akman D.; Tüzün E.; Şanli Erkekoğlu G.; Buran Z.C.; Öztürk Arikan Z.Ö.; Karadağ Yalçin F.
    In this study, it was aimed to evaluate one-year follow-up of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) specific antibodies formed against the virus binding site, in a coronavirus disease-2019 (COVID-19) positive case cohort (n= 413) between the period March 2020 to December 2020 in Manisa Celal Bayar University Hospital, until July 2021. SARS-CoV-2 antibodies were determined by the chemiluminescent enzyme immunoassay (CLIA) method. Values of 1.0 and above were considered positive. Chi-square tests and Joinpoint regression analysis (version 4.7.0) were used in the statistical analyses. The mean age of the participants was 34.9 ± 9.3 and 60.2% of them were women. Between 21-30 days after the diagnosis of COVID-19, total antibody level was above the threshold value in 72.2% (n= 126) of the participants, while this rate increased to 79.1% (n= 240) in 31-60 day interval. In the following period, this rate decreased to 38.8% (n= 108) in days 211st to 240th. Antibody response could not be detected in 76 (20.7%) of 367 employees who have initially been followed up. The percentage of total antibody positivity prevalence ranged from 98.9% to 96.1% in the 31-210th day after diagnosis, in the follow-up of 291 employees whose total antibody positivity was detected after diagnosis. According to the results of the Joinpoint regression analysis, after the diagnosis of COVID-19, the curve showing the percentage of antibody positivity was broken at two points: The first breaking point was observed in 181-210th days (6-7 months) (p= 0.069), and the second breaking point was in 271-300th days (9-10 months) (p< 0.001). As a result, the highest antibody positivity rates were detected after the 30th day of the disease onset and antibody positivity was maintained in the first seven months after diagnosis; the antibody positivity rate decreased to 25% at the end of the first year. © 2022 Ankara Microbiology Society. All rights reserved.
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    Seasonal Trends and Interactions of Viral Pathogens in Children Presenting with Acute Respiratory Tract Infections in the Advancing Periods of SARS-Cov-2 Pandemic; [SARS-CoV-2 Pandemisinin İlerleyen Dönemlerinde Akut Solunum Yolu Enfeksiyonu ile Başvuran Çocuklarda Viral Patojenlerin Mevsimsel Eğilimleri ve Etkileşimleri]
    (Ankara Microbiology Society, 2023) Türkmen Recen Ö.; Gazi H.; Bayturan Şen S.; Bal A.; Akçali S.
    Although various bacteria and viruses have been identified in the etiology of acute respiratory tract infections (ARI), 90% of acute ARIs that develop in children are of viral origin. The aim of this study was to investigate the seasonal trends and interactions between infectious agents and to determine the risk factors associated with ARI in children aged 1-15 years admitted to the Pediatric Emergency Department of Manisa Celal Bayar University Hospital in the advancing periods of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. To determine the bacterial and viral agents, samples were taken from 314 patients attending to the hospital with symptoms suggestive for ARI, between 06/01/2021 and 05/31/2022. Viral and bacterial agents were identified by multiplex polymerase chain reaction (PCR) and automated identification system, respectively. Demographic data of the participants and possible risk factors for ARI were recorded in the questionnaires. In the study, viral agents were detected in 77.3% of the children, and the most common infectious agent was rhinovirus/enterovirus (RV/EV) (36.3%), followed by influenza viruses (11.2%), and SARS-CoV-2 (10.5%). While RV/EV positivity was found to be higher in children with moderate and below average (p< 0.001) hand hygiene, influenza positivity was found higher in those attending school/preschool institution (p< 0.001) and whose mothers working full-time (p< 0.001). Respiratory syncytial virus positivity was associated with maternal smoking (p= 0.013) and home overcrowding (p= 0.014). Bacterial colonization was detected in 33 (11.6%) of 284 children whose swabs were taken for both bacterial and viral agents and the most frequently detected agents were Staphylococcus aureus (60.6%) and Pseudomonas aeruginosa (15.2%). Having siblings (p= 0.008) and maternal smoking (p= 0.012) were found to be associated with the detection of bacterial agents. In this study, in the advanced period of the pandemic, the most detected agents and seasonal characteristics were found to be similar to the pre-pandemic period. It is thought that knowing the regional etiology and risk factors will contribute to taking the necessary local control and protective measures. © 2023 Ankara Microbiology Society. All rights reserved.
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    Efficacy of Homologous and Heterologous Vaccine Applications on SARS-CoV-2 Omicron Variant: Cohort of Manisa Celal Bayar University Healthcare Workers; [Homolog ve Heterolog Aşı Uygulamalarının SARS-CoV-2 Omicron Varyantı Üzerindeki Etkililiği: Manisa Celal Bayar Üniversitesi Sağlık Çalışanları Kohordu]
    (Ankara Microbiology Society, 2023) Çi̇Çek K.; Özkaya Y.; Eser E.; Buran Z.C.; Öztürk Arikan Z.Ö.; Akçali S.; Erbay Dündar P.; Cengi̇Z Özyurt B.; Şenol Akar Ş.; Özer D.; Karadağ Yalçin F.
    This study was aimed to determine the efficacy of homologous (only CoronaVac or only Pfizer-BioNTech) and heterologous (CoronaVac and Pfizer-BioNTech) vaccines during the period when the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron variant was dominant in Türkiye. Coronavirus disease-2019 (COVID-2019) infection was confirmed by reverse transcriptase polymerase chain reaction and data on vaccination status against COVID-19 were evaluated during the period of 15 January 2022-1 May 2022 when the SARS-CoV-2 Omicron variant was dominant among 1854 employees followed in the SARS-CoV-2 Vaccine Cohort of Manisa Celal Bayar University (MCBU) Hospital Health Workers. Two separate reference groups were used in the evaluation of vaccine efficacy: those who were never vaccinated and those who received only two doses of CoronaVac. The efficacy of homologous and heterologous vaccine models was evaluated with relative risks and attributable risk percentages. MS Excel, SPSS 23.0 and STATA 14.1 package programs were used for statistical analysis. The mean age of the participants was 36.6 ± 10.0. During the period from January 15th to May 1st 2022, 372 hospital workers were infected with COVID-19. Taking the never vaccinated as the reference group, the most effective model was found to be only the three or more doses of the Pfizer-BioNTech primary vaccination model (85.8%, 95% CI= 40.7-96.6). Models consisting of a single dose of CoronaVac (6.5%, 95% CI= -56.3-44.2) or a single dose of Pfizer-BioNTech (17.7%, 95% CI= -30.2-48.0) booster dose administered after two doses of primary CoronaVac vaccination was not found to be effective against the SARS-CoV-2 Omicron variant. When only two doses of primary CoronaVac vaccination model was taken as the reference group, the model consisting of two doses CoronaVac followed by two Pfizer-BioNTech booster doses was effective as 38.4% (95% CI= 15.4-55.3), whereas three doses of Pfizer-BioNTech booster model was effective as 56.4% (95% CI= 33.9-71.3). To conclude, none of the models other than the homologous or heterologous vaccine models containing at least three doses of Pfizer-BioNTech vaccine were effective compared to those unvaccinated. Compared with those who received only two doses of primary Coronavac, models with at least three doses of Pfizer-BioNTech reminder doses were more effective against the Omicron variant than other models. © 2023 Ankara Microbiology Society. All rights reserved.