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  1. Article: Türkiye’den Bildirilen Sars-CoV-2 İzolatlarında RT-PCR Primer/Prob Bağlanma Bölgelerindeki Nükleotit Değişimlerinin Analizi.

    Demir, Ayşe Banu / Bulgurcu, Alihan / Appak, Özgür / Sayıner, Ayça Arzu

    Mikrobiyoloji bulteni

    2021  Volume 55, Issue 3, Page(s) 311–326

    Abstract: The SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by ... ...

    Title translation Analysis of Nucleotide Changes in RT-PCR Primer/Probe Binding Regions in SARS-CoV-2 Isolates Reported from Turkey.
    Abstract The SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by real-time reverse transcription polymerase chain reaction (rRT-PCR). However, due to the nature of the RNA viruses, frequent mutations may affect the sensitivity of the analyses made on the genetic material of the virus, such as PCR. In this study, we aimed to investigate the mutations in the primer-probe binding regions of the rRT-PCR panels used in COVID-19 diagnosis. SARS-CoV-2 whole genome sequence data (n= 194) isolated from COVID-19 cases in Turkey and uploaded on GISAID database from the centers in İstanbul (n= 78), Ankara (n= 58), Kars (n= 47), Bursa (n= 2), Adıyaman (n= 2), Erciyes (n= 1) and Kocaeli (n= 1) between March 17-September 14, 2020 were analyzed. In order to determine the nucleotide changes, SARS-CoV-2 sequences from Turkey were compared to the reference genome sequence (NC_045512.1) present in "GenBank" website. The constructed data set was aligned using the MAFFT program and was checked manually if the sequences were in the same frame by using the AliView program. Primer-probe binding sites of the thirteen SARS-CoV-2 rRT-PCR panels from seven different institutes (US CDC, China CDC, Charite CDC, Pasteur, HKU, Thailand, NIID) that are being used in COVID-19 diagnosis were evaluated in terms of nucleotide changes within the corresponding regions compared to the reference genome. Sequence diversities in the viral genomes were determined via positional nucleotide numerical calculator and entropy calculator modules and nucleotide and entropy changes in primer-probe binding regions for each rRT-PCR panel were examined. Among thirteen different primer-probe panels, nucleotide changes in the target regions of the seven primer-probe panels were determined. When viral sequences with nucleotide changes in the primer-probe binding regions were examined, the most common changes were observed in the "China CDC" N-forward primer and "US CDC" N3-forward primer binding regions. It is important that the kits to be used as diagnostic tests are designed specific to the regions with less nucleotide changes. Nucleotide changes may not be critical for DNA amplification for most PCR panels, but should be carefully monitored as they may affect the sensitivity of the assay. If the risk of alteration of the designed region is high, the primer - probe binding sites should be checked frequently and updated when necessary.
    MeSH term(s) COVID-19 ; COVID-19 Testing ; Humans ; Nucleotides ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2 ; Sensitivity and Specificity ; Turkey
    Chemical Substances Nucleotides
    Language Turkish
    Publishing date 2021-08-20
    Publishing country Turkey
    Document type Journal Article
    ZDB-ID 985146-x
    ISSN 0374-9096
    ISSN 0374-9096
    DOI 10.5578/mb.20219803
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  2. Article ; Online: Electromechanical RT-LAMP device for portable SARS-CoV-2 detection.

    Tarim, E Alperay / Oksuz, Cemre / Karakuzu, Betul / Appak, Ozgur / Sayiner, Ayca Arzu / Tekin, H Cumhur

    Talanta

    2022  Volume 254, Page(s) 124190

    Abstract: Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal ... ...

    Abstract Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 10
    Language English
    Publishing date 2022-12-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1500969-5
    ISSN 1873-3573 ; 0039-9140
    ISSN (online) 1873-3573
    ISSN 0039-9140
    DOI 10.1016/j.talanta.2022.124190
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  3. Article: Epidemiology and Acute Respiratory Distress Syndrome Propensity of Viral Respiratory Infections in Pediatric Intensive Care Units Prior to the Coronavirus Disease 2019 Pandemic

    Evren, Gültaç / Besci, Tolga / Appak, Özgür / Sayıner, Ayça Arzu / Arslan, Gazi / Duman, Murat

    Journal of Pediatric Infectious Diseases

    2023  Volume 18, Issue 02, Page(s) 71–76

    Abstract: Objective: This study aimed to determine the epidemiology and acute respiratory distress syndrome (ARDS) propensity of common respiratory viruses in a tertiary pediatric intensive care unit (PICU) among hospitalized children who were tested for ... ...

    Abstract Objective: This study aimed to determine the epidemiology and acute respiratory distress syndrome (ARDS) propensity of common respiratory viruses in a tertiary pediatric intensive care unit (PICU) among hospitalized children who were tested for respiratory viruses by polymerase chain reaction (PCR) prior to the coronavirus disease 2019 (COVID-19) pandemic.
    Methods: Respiratory tract samples were collected from patients who were followed up in the Dokuz Eylul University Hospital pediatric intensive care unit between March 2015 and March 2020 and tested for viral pathogens. The results of 269 patients between 1 month and 18 years of age were evaluated retrospectively.
    Results: In the 5 years preceding the COVID-19 pandemic, 269 patients with a lower respiratory infection were admitted to the PICU. A positive viral PCR result was detected in 160 patients (59.5%). Human rhinovirus was the most common virus (40%), followed by respiratory syncytial virus (26.3%), human bocavirus (10%), and seasonal coronaviruses (10%). Five (33.3%) of the fifteen children who developed ARDS were infected with influenza A/B, while four (26.7%) were infected with human metapneumovirus (hMPV).
    Conclusion: Although rhinovirus was the most common viral agent in critically ill children, the incidence of ARDS was higher in children aged over 1 year who had influenza or hMPV infection.
    Keywords virus ; respiratory infection ; pediatric intensive care ; epidemiology ; ARDS
    Language English
    Publishing date 2023-01-05
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 2236947-8
    ISSN 1305-7693 ; 1305-7707 ; 1871-0336
    ISSN (online) 1305-7693
    ISSN 1305-7707 ; 1871-0336
    DOI 10.1055/s-0042-1760410
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  4. Article: Viral Etkenlere Bağlı Santral Sinir Sistemi Enfeksiyonlarının Yedi Yıllık Değerlendirmesi.

    Varıcı Balcı, Fatma Kamer / Sayıner, Ayça Arzu

    Mikrobiyoloji bulteni

    2019  Volume 53, Issue 4, Page(s) 434–441

    Abstract: Identification of viral agents causing central nervous system (CNS) infections increased by the application of nucleic acid tests. In this study, the results of polymerase chain reaction (PCR) for viral agents were evaluated in cerebrospinal fluid (CSF) ... ...

    Title translation A Seven-Year Evaluation of Viral Central Nervous System Infections.
    Abstract Identification of viral agents causing central nervous system (CNS) infections increased by the application of nucleic acid tests. In this study, the results of polymerase chain reaction (PCR) for viral agents were evaluated in cerebrospinal fluid (CSF) samples taken from patients with CNS infection. CSF samples taken from 1185 patients between 2010 and 2017 were tested for the presence of Herpes simplex virus (HSV) type 1 and 2, Varicella Zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), adenovirus ve enterovirus by PCR in Dokuz Eylul University Hospital. Tests were performed according to the clinicians' orders and results were evaluated retrospectively. The number of tests performed were 1038 for HSV, 882 for adenovirus, 865 for enterovirus, 496 for VZV, 100 for EBV and 92 for CMV. Commercial tests were used for EBV, CMV (Artus QS-RGQ Kits, Qiagen, Germany) and enterovirus (GeneXpert, Cepheid, USA) while the other viruses (HSV, VZV, adenovirus) were tested by in-house real-time PCR assays. Ninety-one CSF (7.7%) samples were positive. The mean age was 13 (<1 to 76 years) while median was seven. The most frequently detected pathogens were enterovirus (63/91, 69%) and HSV-1 (14/91,15%). The number of patients positive for adenovirus, VZV, EBV and CMV were five, four, three and two, respectively. In one patient, both enterovirus (Ct: 29.5) and EBV (Ct: 38.53) were positive. The number of positive samples were increased in summer months. Enterovirus RNA positive patients (n= 60/63, 95.2%) were ≤ 18 years old while 29% were younger than one year of age. Enterovirus positive samples peaked in 2012 and 2014 and detected mainly in summer (60.3%) and autumn (20.6%) months. VZV was mostly detected in patients greater than 65 years of age. Mean Ct of the positive reactions was 31.87 ± 3.5 (22.88-40.32). The lowest and the highest Ct values were detected in HSV-1 assay. The mean Ct value of enterovirus assay (30.4; 25.7-35.9) was lower than the other pathogens' values. In the seven-year period, 7.7% of the1185 patients' CSF samples were positive for viral nucleic acids. As expected, enteroviruses were the most common pathogens in children and detected mainly in summer-autumn period. Syndromic approach in CNS infections could increase the viral pathogen detection.
    MeSH term(s) Adolescent ; Adult ; Aged ; Central Nervous System Viral Diseases/cerebrospinal fluid ; Central Nervous System Viral Diseases/epidemiology ; Central Nervous System Viral Diseases/virology ; Child ; Child, Preschool ; DNA, Viral/genetics ; Germany/epidemiology ; Humans ; Infant ; Middle Aged ; Polymerase Chain Reaction ; Retrospective Studies ; Viruses/genetics ; Young Adult
    Chemical Substances DNA, Viral
    Language Turkish
    Publishing date 2019-11-09
    Publishing country Turkey
    Document type Journal Article
    ZDB-ID 985146-x
    ISSN 0374-9096
    ISSN 0374-9096
    DOI 10.5578/mb.68012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Genetic diversity of Pneumocystis jirovecii isolates among Turkish population based on mitochondrial large subunit ribosomal RNA and dihydropteroate synthase gene typing.

    Gurbuz, Ceren Erguden / Delibas, Songul Bayram / Alpaydin, Aylin Ozgen / Sayiner, Ayca Arzu / Ozkoc, Soykan

    Medical mycology

    2021  Volume 59, Issue 8, Page(s) 813–820

    Abstract: Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause severe interstitial pneumonia in immunocompromised patients. In this study, mitochondrial large subunit ribosomal RNA (mtLSU-rRNA) and dihydropteroate synthase (DHPS) gene ... ...

    Abstract Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause severe interstitial pneumonia in immunocompromised patients. In this study, mitochondrial large subunit ribosomal RNA (mtLSU-rRNA) and dihydropteroate synthase (DHPS) gene polymorphism in P. jirovecii isolates were investigated in Western Turkey's Izmir province and its surroundings. For this purpose, a total of 157 P. jirovecii isolates obtained from bronchoalveolar lavage samples of hospitalized cases and lung tissue samples of autopsy cases who died outside hospital were examined. Genotypes were identified by direct sequencing of mtLSU-rRNA restriction fragment length polymorphism analysis of the DHPS gene amplicons. The mtLSU-rRNA analysis revealed that genotype 2 was the most common genotype with 58%. The following genotypes were genotype 3 (13%), genotype 1 (11.6%) and genotype 4 (5.1%), while genotype 5 (0.7%) was detected in only one autopsy case. In addition, 16 (11.6%) cases had dual or triple different genotypes (mixed infection). It was observed that the genotype distribution was not affected by characteristics such as age, gender and immune status. However, the predominance of genotype 2 in solid organ tumors and the predominance of mixed infection in patients with chronic pulmonary disease were statistically significant. On the other hand, DHPS gene amplification was positive in 137 (87.3%) of 157 samples. While no mutation was observed in 135 samples, the association of wild-type and 57th codon mutation was detected in two hospitalized cases (1.5%). In this study, important epidemiological data on the distribution of mtLSU-rRNA genotypes were obtained. Also the existence of DHPS gene mutations associated with potential drug resistance in our community was shown for the first time. Further studies are needed to evaluate the possible effects of genotypes on the prognosis of the disease to help with the clinician's treatment decisions.
    Lay abstract: Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause life-threatening pneumonia in immunocompromised patients. In this study, we investigated the mtLSU-rRNA and DHPS gene polymorphisms in P. jirovecii isolates from both hospital and autopsy cases.
    MeSH term(s) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Dihydropteroate Synthase/genetics ; Female ; Genetic Variation ; Genotyping Techniques ; Humans ; Infant ; Male ; Middle Aged ; Mitochondria/genetics ; Pneumocystis carinii/classification ; Pneumocystis carinii/enzymology ; Pneumocystis carinii/genetics ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Turkey
    Chemical Substances RNA, Ribosomal ; Dihydropteroate Synthase (EC 2.5.1.15)
    Language English
    Publishing date 2021-02-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 1421796-x
    ISSN 1460-2709 ; 1369-3786
    ISSN (online) 1460-2709
    ISSN 1369-3786
    DOI 10.1093/mmy/myab004
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    Zs.A 520: Show issues Location:
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  6. Article: Distribution of Viral Respiratory Pathogens During the COVID-19 Pandemic: A Single-Center Pediatric Study from Turkey.

    Şık, Nihan / Çakan Başerdem, Kevser Asena / Başerdem, Oğuzhan / Appak, Özgür / Sayıner, Ayça Arzu / Yılmaz, Durgül / Duman, Murat

    Turkish archives of pediatrics

    2022  Volume 57, Issue 3, Page(s) 354–359

    Abstract: Objective: To evaluate the distribution and characteristics of respiratory viral pathogens and to assess the epidemiological data, clinical features, and prognoses of infected children in a pediatric emergency department during the COVID-19 pandemic.: ...

    Abstract Objective: To evaluate the distribution and characteristics of respiratory viral pathogens and to assess the epidemiological data, clinical features, and prognoses of infected children in a pediatric emergency department during the COVID-19 pandemic.
    Materials and methods: Between September 1, 2020, and April 30, 2021, patients aged between 0 and 18 years arrived at the pediatric emergency department and were tested by nasopharyngeal/tracheal specimen polymerase chain reaction for both SARS-CoV-2 and other viral respiratory pathogens. Demographics, symptoms, laboratory and radiologic investigations, respiratory viruses detected by PCR, presence of co-infection and co-infecting viruses, need for respiratory support, hospitalization, length of hospital stay, and prognosis were recorded.
    Results: There were 327 patients for whom PCR tests were performed and 118 (36.0%) of them had positive results for SARS-CoV-2 and/or other respiratory viruses. Rhinovirus was the most commonly detected pathogen with 74 (62.7%) cases, followed by enterovirus with 38 (32.2%) and adenovirus with 20 (16.9%) cases. There was no detection of influenza virus or respiratory syncytial. SARS-CoV-2 PCR results were positive in 14 (11.9%) cases and there was only 1 coinfection of SARS-CoV-2 occurring together with rhinovirus. For 43 (36.4%) patients, there was co-infection, and among co-infections, the most common was that of rhinovirus and enterovirus, seen in 37 (86.0%) cases.
    Conclusion: A decrease was observed in the positivity rate of respiratory viral pathogens, while no cases of influenza virus or respiratory syncytial virus were observed in our study. Circulating viruses may change due to multifactorial approaches during the COVID-19 pandemic.
    Language English
    Publishing date 2022-06-27
    Publishing country Turkey
    Document type Journal Article
    ISSN 2757-6256
    ISSN 2757-6256
    DOI 10.5152/TurkArchPediatr.2022.21350
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  7. Article ; Online: Hepatitis E Infection in Solid Organ Transplant Recipients in Turkey.

    Öğüt, Seval / Sayıner, Ayça Arzu / Otlu, Barış / Bozdayı, Gülendam / Zeytinoğlu, Ayşın / Aksaray, Sebahat / Çolak, Dilek / Gökahmetoğlu, Selma / Aysın, Murat

    The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology

    2022  Volume 33, Issue 1, Page(s) 68–73

    Abstract: Background: Hepatitis E virus is a re-emerging pathogen with an increase in human cases that can lead to chronic infection in immunosuppressed patients. Turkey is located between Asia and Europe, 2 regions with distinct epidemiological and clinical ... ...

    Abstract Background: Hepatitis E virus is a re-emerging pathogen with an increase in human cases that can lead to chronic infection in immunosuppressed patients. Turkey is located between Asia and Europe, 2 regions with distinct epidemiological and clinical features of hepatitis E virus infection. This multicenter cross-sectional study aimed to investigate the prevalence of hepatitis E virus infection in liver and kidney transplant recipients in Turkey and to determine the role of possible transmission factors.
    Methods: A total of 485 plasma samples of solid organ recipients were collected from 7 transplantation centers in Turkey. Samples were tested for anti-hepatitis E virus immunoglobin M, immunoglobin G, and hepatitis E virus ribonucleic acid. Water- and food-related risk factors were evaluated by a questionnaire.
    Results: Samples of 300 kidney and 185 liver recipients were collected. Hepatitis E virus ribonucleic acid was tested in 472 samples and none were positive. Anti-hepatitis E virus immunoglobin G and immunoglobin M were detected in 84 (17.3%) and 3 (0.6%) patients, respectively. Seropositivity was associated with older age, male gender, being a liver recipient, and being infected with hepatitis B virus and/or hepatitis C virus. None of the patients under the age of 30 were seropositive. Hepatitis E virus immunoglobin G prevalence was higher in the Central East and Southeast Anatolia. Eating raw meat was the only independent variable associated with hepatitis E virus seropositivity.
    Conclusion: This is the first prevalence study of hepatitis E virus infection in solid organ recipients in Turkey. Anti-hepatitis E virus immunoglobin G prevalence was 17.3% which was higher than the previously reported rate in blood donors. Seropositivity was significantly higher in liver recipients. Despite the high antibody prevalence, none of the patients were viremic.
    MeSH term(s) Cross-Sectional Studies ; Hepatitis E/epidemiology ; Hepatitis E virus/genetics ; Humans ; Male ; Organ Transplantation/adverse effects ; RNA ; Seroepidemiologic Studies ; Transplant Recipients ; Turkey/epidemiology
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2022-01-13
    Publishing country Turkey
    Document type Journal Article ; Multicenter Study
    ZDB-ID 1340275-4
    ISSN 2148-5607 ; 1300-4948
    ISSN (online) 2148-5607
    ISSN 1300-4948
    DOI 10.5152/tjg.2021.21071
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  8. Article ; Online: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients.

    Appak, Özgür / Duman, Murat / Belet, Nurşen / Sayiner, Ayça Arzu

    Journal of medical virology

    2019  Volume 91, Issue 5, Page(s) 731–737

    Abstract: Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent-specific. The aim of this study was to investigate the respiratory viruses in children ... ...

    Abstract Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent-specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real-time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8-year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016-2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.
    MeSH term(s) Adolescent ; Child ; Child, Preschool ; Coinfection/diagnosis ; Coinfection/virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Molecular Diagnostic Techniques/methods ; Multiplex Polymerase Chain Reaction/methods ; Prevalence ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/virology ; Retrospective Studies ; Virus Diseases/diagnosis ; Virus Diseases/virology ; Viruses/classification ; Viruses/genetics ; Viruses/isolation & purification
    Keywords covid19
    Language English
    Publishing date 2019-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.25379
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  9. Article ; Online: Hepatitis A, B and C seropositivity among first-year healthcare students in western Turkey: a seroprevalence study.

    Acikgoz, Ayla / Cimrin, Dilek / Kizildag, Servet / Esen, Nuran / Balci, Pinar / Sayiner, Ayca Arzu

    BMC infectious diseases

    2020  Volume 20, Issue 1, Page(s) 529

    Abstract: Background: The risk of viral hepatitis among healthcare students (HCSs) is greater than that among the general population. Therefore, this study was conducted to investigate the seroprevalence of the hepatitis A virus (HAV), hepatitis B virus (HBV) and ...

    Abstract Background: The risk of viral hepatitis among healthcare students (HCSs) is greater than that among the general population. Therefore, this study was conducted to investigate the seroprevalence of the hepatitis A virus (HAV), hepatitis B virus (HBV) and hepatitis C virus (HCV) among first-year HCSs at a university in Turkey and as a secondary objective, to determine the factors associated with HAV and HBV seropositivity.
    Methods: This cross-sectional study was performed in first-year HCSs in Izmir, western Turkey. Data were collected using a self-administered questionnaire including items on sociodemographic characteristics, medical history, and hygiene. A total of 650 HCSs were tested for the HAV, HBV and HCV markers. Categorical variables were compared using the chi-square test. The association between independent variables and anti-HAV seropositivity and anti-HBs seropositivity was assessed by multinomial logistic regression analysis.
    Results: The overall frequency of total anti-HAV seropositivity was 34.9%. HBsAg, total anti-HBc and anti-HBs seropositivity were found in 0.3, 1.2 and 93.7% of samples, respectively. All of the HCSs were negative for anti-HCV. Total anti-HAV seropositivity was found to be 1.73 times higher in those ≥21 years old, and it was 1.61 times higher in those who perceived their economic status to be average and 2.75 times higher in those who perceived their economic status to be low. Total anti-HAV seropositivity was found to be 4.37 times higher in those who lived in provinces with intermediate human development index levels. Total anti-HBs seropositivity was found to be 2.48 times higher in those ≤20 years old, and it was 2.13 times higher in those who perceived their economic status to be average.
    Conclusions: Approximately two out of three HCSs were susceptible to HAV infection. Since HCSs are at high risk for HAV infection, they should be vaccinated before medical clerkships begin. Our results indicate that there is a high prevalence of anti-HBs seropositivity among HCSs. This result may be largely attributed to the implementation of a successful vaccination program in Turkey since 1998.
    MeSH term(s) Adolescent ; Adult ; Cross-Sectional Studies ; Female ; Hepacivirus/immunology ; Hepatitis A/blood ; Hepatitis A/epidemiology ; Hepatitis A/virology ; Hepatitis A virus/immunology ; Hepatitis B/blood ; Hepatitis B/epidemiology ; Hepatitis B/virology ; Hepatitis B Antibodies/blood ; Hepatitis B Surface Antigens/blood ; Hepatitis B virus/immunology ; Hepatitis C/blood ; Hepatitis C/epidemiology ; Hepatitis C/virology ; Humans ; Immunization Programs ; Male ; Prevalence ; Self Report ; Seroepidemiologic Studies ; Students, Medical ; Turkey/epidemiology ; Young Adult
    Chemical Substances Hepatitis B Antibodies ; Hepatitis B Surface Antigens
    Language English
    Publishing date 2020-07-22
    Publishing country England
    Document type Journal Article
    ISSN 1471-2334
    ISSN (online) 1471-2334
    DOI 10.1186/s12879-020-05247-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Pneumocystis jirovecii Laboratuvar Tanısında Gerçek Zamanlı Polimeraz Zincir Reaksiyonu Yönteminin Değerlendirilmesi.

    Özkoç, Soykan / Ergüden Gürbüz, Ceren / Sayıner, Ayça Arzu / Bayram Delibaş, Songül

    Mikrobiyoloji bulteni

    2020  Volume 54, Issue 3, Page(s) 418–428

    Abstract: Pneumocystis jirovecii is a human-specific species and causes fatal infections like P.jirovecii pneumonia (PCP) in immunocompromised persons. Although direct microscopy is the gold standard in the diagnosis of the microorganism, molecular methods such as ...

    Title translation Evaluation of Real-Time Polymerase Chain Reaction in Pneumocystis jirovecii Laboratory Diagnosis.
    Abstract Pneumocystis jirovecii is a human-specific species and causes fatal infections like P.jirovecii pneumonia (PCP) in immunocompromised persons. Although direct microscopy is the gold standard in the diagnosis of the microorganism, molecular methods such as polymerase chain reaction (PCR) are needed in non-human immune deficiency virus (HIV) immunosuppresive patients with low P.jirovecii burden. In this study, we aimed to evaluate the value of real-time PCR (Rt-PCR) in the laboratory diagnosis of P.jirovecii. Bronchoalveolar lavage (BAL) specimens of 658 patients sent to Dokuz Eylul University Hospital Central Medical Parasitology Laboratory on suspicion of PCP were included in the study. BAL fluids were evaluated for identification of P.jirovecii mitochondrial gene coding ribosomal large subunit (mtLSUrRNA) using Rt-PCR. In addition, Giemsa and Gomori's methenamine silver (GMG) staining assays were applied to all samples and nested PCR (n-PCR) assay was applied to positive samples detected by real time PCR. Ninety-two (14.3%) of these samples were positive by Rt-PCR. Of these 92 patients, 85 (92.4%) were positive with n-PCR. Only seven of the specimens had P.jirovecii cysts and trophozoites with microscopic examination. The mean cycle threshold (CT ) value of Rt-PCR positive patients was 29.7 (18.17 ≤ CT ≤ 37.96). P.jirovecii load in these patients was calculated as 2.6 x 101-6.15 x 107 copies/ml. The difference between the mean CT values of n-PCR positive and negative results was statistically significant (p< 0.01). The CT values of Rt-PCR of the samples with positive microscopy were; 18.2, 20.9, 22.2, 24.3, 24.7, 26.5, 29.7. The difference between the CT means of the samples with positive and negative microscopy was statistically significant (p< 0.05). When positive patients were grouped according to their diagnosis; the lowest mean CT value (CTmean= 24.8) was found in HIV-positive patients. On the other hand, CT values were found to be significantly lower in the organ transplantation patients (CTmean= 26.15) and in the collagen-vascular-inflammatory patient group (CTmean= 27.8). This study demonstrated that Rt-PCR was the effective method in the diagnosis of P.jirovecii in the laboratory. Conventional n-PCR method was found to be more unsuccessful than Rt-PCR in the presence of very low density organism; direct microscopy is generally found to be positive in samples with a higher burden of P.jirovecii.
    MeSH term(s) Bronchoalveolar Lavage Fluid/microbiology ; Clinical Laboratory Techniques/standards ; Humans ; Pneumocystis carinii/genetics ; Pneumonia, Pneumocystis/diagnosis ; Pneumonia, Pneumocystis/microbiology ; Real-Time Polymerase Chain Reaction/standards ; Sensitivity and Specificity
    Language Turkish
    Publishing date 2020-08-05
    Publishing country Turkey
    Document type Journal Article
    ZDB-ID 985146-x
    ISSN 0374-9096
    ISSN 0374-9096
    DOI 10.5578/mb.69711
    Database MEDical Literature Analysis and Retrieval System OnLINE

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