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Öğe 2019-2021 Yılları Arasında Saptanan Viral Solunum Yolu Enfeksiyonu Etkenleri, COVID-19 ve Ko-Enfeksiyonlar(2023) Aydoğan, Sibel; Kırca, Füsun; Gozalan, Aysegul; Toyran, Alparslan; Başyiğit, Tuğcan; Omay, İpek; Dinc, BediaSolunum yolu enfeksiyonları, her yaşta önemli morbidite ve mortalite nedeni olup tüm dünyada çok önemli bir halk sağlığı sorunu olarak görülmektedir. Bu çalışmada, pandemi öncesi bir yıllık dönemi de içine alan üç yıllık dönemde moleküler mikrobiyoloji laboratuvarında multipleks polimeraz zincir reaksiyonu [polymerase chain reaction (PCR)] testi ile çalışılan solunum yolu viral enfeksiyon etkenlerinin, viral koenfeksiyonların ve Koronavirüs hastalığı-2019 [Coronavirus disease-2019 (COVID-19)] ile birlikteliklerinin analizini yaparak pandeminin, etkenlerin epidemiyolojik ve mevsimsel özellikleri üzerine olan etkisinin değerlendirilmesi amaçlanmıştır. Mart 2019-Aralık 2021 tarihleri arasında moleküler mikrobiyoloji laboratuvarına solunum yolları multipleks PCR test istemiyle kabul edilen 8825 solunum yolu örneği çalışmaya alınmıştır. Ayrıca solunum yolları multipleks PCR testiyle pozitif sonuç alınmış hastaların ± 3 gün içinde çalışılmış şiddetli akut solunum yolu sendromu koronavirüs-2 [severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)] PCR testi sonuçları retrospektif olarak değerlendirilmiştir. Solunum yolu viral patojenleri “FTD Respiratory Pathogens 21 kit (Fast Tract Diagnostics, Siemens Healthineers, Almanya)” ile çalışılarak tespit edilmiştir. SARS-CoV-2 RNA saptanması için farklı dönemlerde gerçek zamanlı revers transkriptaz PCR esaslı iki ayrı kit kullanılmıştır. Çalışmada elde edilen bulgulara göre, 8825 örneğin 2156 (%24.4)’sında en az bir viral etken ve bunların 1843 (%85.5)’ünde tek etken saptanmıştır. Tek etken saptanan örneklerdeki virüslerin dağılımı sıklık sırasına göre RV, RSV A/B, HCoVs, AdV, flu A virüsü, MPV A/B, PIV 1-4, flu B virüsü, EV, BoV ve PeV olarak belirlenmiştir. Etken saptanan 2156 hasta örneğinin 313 (%14.5) tanesinde çoklu etken bulunmuştur. Bunlar; 291 örnekte iki, 21 örnekte üç ve bir örnekte dört etken olarak görülmüştür. En sık saptanan kombinasyonlar AdV + RV, AdV + EV, EV + RV, RV + HCoVs, RSV A/B + RV olarak saptanmıştır. Solunum yolları multipleks PCR ile pozitif sonuç alınmış hastaların ± 3 gün içinde çalışılmış SARS-CoV-2 PCR test sonuçları retrospektif olarak değerlendirildiğinde, en az bir etken saptanmış 1277 örneğin 45 (%3.5)’inde SARS-CoV-2 RNA tespit edilmiştir. Bu hastaların dört tanesinde SARS-CoV-2 çoklu etkenlerle birlikte bulunmuştur. Sonuç olarak, pandemi döneminde tüm viral etkenlerin prevalansında keskin bir azalma görülmüştür. Bu duruma, COVID-19 enfeksiyonunun yanı sıra pandemi döneminde uygulanan kısıtlamaların da etkili olduğu düşünülmüştür.Öğe Comparison of clinical characteristics of wild-type SARS-CoV-2 and Omicron(2022) Kırca, Füsun; Aydoğan, Sibel; Gözalan, Ayşegül; Kayıpmaz, Afşin Emre; Özdemir, Fatma Ayça Edis; Tekçe, Yasemin Tezer; Beşer, İpek Omay; Gün, Pınar; Ökten, Rıza Sarper; Dinç, BediaOBJECTIVE: This study aimed to investigate the effect of mutations by comparing wild-type SARS-CoV-2 and Omicron regarding clinical features in patients with COVID-19. It also aimed to assess whether SARS-CoV-2 cycle threshold value could predict COVID-19 severity. METHODS: A total of 960 wild-type and 411 Omicron variant patients with positive results in SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction test from oropharyngeal and/or nasopharyngeal samples during their hospital admissions were included in this retrospective study. The reference symptoms of the patients were obtained from the hospital database. The correlation between chest computed tomography findings and the "cycle threshold" of patients with wild-type SARS-CoV-2 was assessed. RESULTS: Cough, fever, shortness of breath, loss of taste and smell, and diarrhea were found to be statistically significantly higher (p=0.001; 0.001; 0.001; 0.001; and 0.006; respectively) in the wild-type cohort, while in the Omicron cohort, sore throat and headache were found to be statistically significantly higher (p=0.001 and 0.003, respectively). An inverse relationship was found between chest computed tomography findings and viral load. CONCLUSION: This study revealed that the Omicron variant tended to infect predominantly the upper respiratory tract and showed decreased lung infectivity, and the disease progressed with a milder clinical course. Therefore, the study showed that the tropism of the virus was changed and the viral phenotype was affected. It was also found that SARS-CoV-2 viral load did not predict COVID-19 severity in patients with wild-type SARS-CoV-2.Öğe Investigation of Legionella pneumophila and other Legionella species in atypical pneumonia patients(2022) Parlak, Kerim; Gözalan, Ayşegül; Aydoğan, Sibel; Koyuncu, Adem; Hasanoğlu, Hatice Canan; Nar Ötgün, Selin; Açıkgöz, Ziya CibaliObjective: The aim of this study is to investigate Legionella species in 50 patients with atypical pneumonia, using culture, urinary antigen test and molecular techniques. Methods: Non-selective BCYE-? media (Oxoid, England) and selective BMPA media (Oxoid, England) were used to isolate Legionella spp. from respiratory tract samples. The urinary samples of the patients were tested with the Alere BinaxNOW Legionella Urinary Antigen Card (Abbott, US) test to identify the presence of L. pneumophila serogroup 1 specific bacterial antigen. All respiratory tractsamples were tested with a commercial Duplic? RealTime Legionella pneumophila 23S rRNA specific region detection kit (Euroclone Diagnostica, Italy) and two home-made PCR methods. Home-made gel electrophoresis PCR tests were performed using Leg primers designed from 16S ribosomal RNA gene partial sequences for Legionella spp and primers targeting the Lmip (macrophage infectivity potentiator) gene for L. pneumophila. In the home-made real-time PCR test, primers targeting the lipopolysaccharide (lps) biosynthesis gene of L. pneumophila serogroup-1, the L. pneumophila mip gene, and the Legionella spp DNA region encoded by the 16S ribosomal RNA gene were used. Results: The commercial Real-time PCR assay identifed the sequence of L. pneumophila 23S rRNA gene specific region in seven respiratory tract samples. Five samples were detected as Legionella spp. in home-made gel electrophoresis-based PCR and home-made Real-time PCR assay. Hovewer, all samples tested negative in the urinary antigen card test for L. pneumophila serogroup 1. Conclusion: We conclude that the PCR positivities with three different molecular methods indicate that Legionella species other than L. pneumophila serogroup 1 should be investigated in the patients with atypical pneumonia using molecular methods. Also, our study demonstrates the significance of PCR methods in the investigation of Legionella species in clinical samples taken from patients with negative test results for L. pneumophila serogroup 1 specific urinary antigen test, but who are clinically considered to have Legionella pneumoniae.Öğe The identification of acinetobacter baumannii blood isolates by MALDI-TOF MS, ARDRA and bla(OXA-51-like) Gene-Specific Real-Time PCR(Ankara Microbiology Soc, 2020) Gözalan, Ayşegül; Aydoğan, Sibel; Hacıseyitoğlu, Demet; Kuzucu, Çiğdem; Köksal, Fatma; Açıkgöz, Ziya Cibali; Durmaz, RızaThe Acinetobacter cakoaceticus-Acinetobacter baumannii (Acb) complex consists of phenotypically very similar nosocomial species; A.baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter djikshoorniae and one environmental species Acakoaceticus. The rapid and accurate identification of the members of Acb complex is critical as these nosocomial pathogens can show differences in antimicrobial susceptibility and clinical outcomes. The conventional phenotypic methods are slow, unreliable and less efficient for the differentiation of Acb complex species, including the A.baumannii species within the Acb complex. Although various molecular methods are available, such as amplified ribosomal DNA restriction analysis (ARDRA) and bla(OXA-51-like), gene specific PCR, they are usually inconvenient for the routine diagnostic laboratories. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers an opportunity for rapid, cost-effective and convenient bacterial identification in routine diagnostic procedures conducted in clinical laboratory. In this study, we aimed to evaluate the diagnosis performance of MALDI-TOF MS system to identify blood isolates of A.baumannii. A total of 180 nonduplicate carbapenem resistant Acb complex (strain numbers; TR1-TR60) and A.baumannii (TR61-TR180) blood isolates were collected from the intensive care units of the three university hospitals in Turkey from January 2016 to December 2016. All isolates were evaluated by using bla(OXA-51-like) gene specific real time (Rt-PCR) analysis, ARDRA (restriction enzymes-AIM, Cfol, Mbol, Mspl, Rsal) method and MALDI-TOF MS (VITEK (R) MS, bioMerieux, France) system. All the strains except TRIO, TR31, TR35 and TR52 were identified as A.baumannii by ARDRA method. Out of 177 of all the isolates, presence of bla(OXA-51-like) gene was found except for TR10, TR31 and TR52 isolates. However, TR31 without the presence of bla(OXA-51-like) gene was identified as A.pittii using the ARDRA. Totally 176 isolates which were identified as A. baumannii by both of the methods, ARDRA and Rt-PCR-bla(OXA-51-like) ,were accepted as a reference for the evaluation of the diagnosis performance capacity of the MALDI-TOF MS. Overall, for all 176 isolates tested, the sensitivity obtained with the MALDI-TOF MS were 99.4% with 75% specificity. The accuracy value of the method was determined as 98.9% for the identification of A.baumannii to the species level. MALDI-TOF MS is increasingly used in diagnostic microbiology for the routine identification of bacteria to the genus, species or subspecies level with high rates of sensitivity and specificity. In future, by expanding the database, MALDI-TOF MS system would possibly become the ideal method for routine diagnostic laboratories that could potentially identify more species and even determine some characteristics of antimicrobial resistance and virulence determinants.
