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Öğe An Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) Outbreak in Intensive Care Units and Infection Control Measures(2022) Erdem, Fatma; Bozok, Taylan; Kalaycı, Yıldız; Öcal, Melda Meral; Ünal, Nevzat; Köksal, FatihIntroduction: Elizabethkingia meningoseptica is an emerging gram-negative opportunistic nosocomial pathogen reported in immunocompromised patients. We aimed to report an outbreak of E. meningoseptica acquisition in the intensive care units (ICUs) of a training and research hospital in Turkey and highlight the infection control measures. Materials and Methods: Bacterial strains were determined using MALDI Biotyper (Bruker Daltonics, Bremen, Germany) minimum inhibitor concentrations were examined using MicroScan automatized system. Results were determined according to the CLSI guidelines. Environmental cultures were obtained and investigated for the presence of E. meningoseptica. Clonal relationships among E. meningoseptica strains were investigated using PFGE. Results: Isolates were obtained from nine critically ill patients’ clinical samples. All strains were resistant to tested antibiotics (amikacin, Amox/Clav, cefepime, cefotaxime, ceftzidime, cefuroxime, ertapenem, gentamycin, meropenem, trimethoprim/sulfamethoxazole (TMP–SMX), imipenem) except for levofloxacin (8/9), ciprofloxacin (5/9), and piperacillin/tazobactam. PFGE indicated that the strains involved in the outbreak were closely related. Conclusion: Intrinsically multiple drug-resistant Elizabethkingia spp. isolates can be a common life-threatening pathogen in ICUs in our country, and prevention is possible through early notification of small-scale outbreaks and necessary infection control measures.Öğe Comparative Analysis of the Effect of Different Nucleic Acid Extraction Methods on SARS-CoV-2 Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction Results(Ankara Microbiology Soc, 2023) Bozok, Taylan; Ozturk, AliSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of Coronavirus diseases-2019 (COVID-19) disease. Rapid and accurate detection of the virus is vital to prevent transmission and effectively manage the pandemic. The gold standard diagnostic method for this agent is the real-time reverse transcription polymerase chain reaction (qrRT-PCR) test conducted on respiratory tract samples and one of the most critical steps affecting the sensitivity of this test is the nucleic acid extraction stage. However, restrictive factors such as reagent supply and storage conditions limit the testing capacity. Therefore, innovative and cost-effective alternatives are needed to speed up testing and minimize pre-processing steps. The aim of this study was to evaluate the impact and applicability of different methods to enhance the efficiency of the nucleic acid extraction stage in the SARS-CoV-2 qrRT-PCR test. As an alternative to the routinely used viral nucleic acid extraction buffer (vNAT), the modified vNAT method (MvNAT), which includes centrifugation, the R1-R2 kit and the heat treatment (HT) method, was applied to 118 respiratory tract samples. Samples determined with threshold cycle values of (Cq) of <= 35 (n= 10), > 35 (n= 42), indeterminate (n= 56) in routine results and negative controls (n= 10) were included in the study. The RNA quantities obtained after extraction for each method were measured and recorded using a spectrophotometric measurement device. All samples were processed using the SARS-CoV-2 qrRT-PCR kit targeting the RdRp region. The results were statistically analyzed using unpaired and paired t-tests and results with a p-value of < 0.05 were considered statistically significant. Excluding negative control samples, while the standard method yielded a Cq value of 48.1% (mean Cq value (Cq(mean))= 39.5 +/- 6.9) for a total of 108 samples, the MvNAT method produced a Cq value of 11.1% (Cq(mean)= 38.4 +/- 5.2), the R1-R2 kit yielded 14.8% (Cq(mean)= 35.9 +/- 7.1) and HT method resulted in 25% (Cq(mean)= 31.4 +/- 6.3). When the variability in target gene Cq values was analyzed in all samples compared to the standard method, the HT method significantly provided lower Cq values (n= 16; p= 0.007; paired t-test) while the MvNAT method and R1-R2 kit yielded higher Cq values (n= 6; p= 0.025, n= 11; p= 0.004; paired t-test). Sensitivity rates were MvNAT= 31.6%, R1-R2= 57.9%, HT= 84.2%, with 100% specificity for all three methods. The HT method demonstrated a positive extraction efficiency because it is fast, easy and not dependent on reagents. Although this method provided lower Cq values than the standard method, especially in samples with a high viral load, it should be considered that it also has the potential to yield false-negative results in samples with Cq> 35. With this study, it was concluded that the extraction phase of the SARS-CoV-2 qrRT-PCR test can be carried out using various methods that do not require kits or reagents, such as the HT method. However, it is believed that multicenter studies involving a larger number of samples are necessary to standardize the test and assess the possibility of false negatives.Öğe COVID-19 Hastalarının Alt Solunum Yolu Örneklerinden İzole Edilen Bakteriyel Etkenlerin İdentifikasyonu ve Antibakteriyel Direnç Paternlerinin İncelenmesi(2022) Avan, Tuğba; Bozok, TaylanAmaç: Bu çalışmada amaç, COVID-19 hastalığı nedeni ile yatan hastalarda meydana gelen sekonder bakteriyel enfeksiyon etkenlerini tanımlamak ve bu etkenlerin antibakteriyel direnç durumlarını belirlemektir. Böylece sekonder enfeksiyon düşünülen hastalarda başlanacak ampirik tedavi için öngörü sağlanarak gereksiz antibiyotik kullanımı önlemede katkıda bulunulacaktır. Yöntem: Çalışmamızda, Mart 2020 ve Şubat 2021 tarihleri arasında Niğde Eğitim ve Araştırma Hastanesi’nde COVID-19 nedeni ile Yoğun Bakım Ünitesi (YBÜ)’nde yatan hastalardan gönderilen alt solunum yolu örneklerinden izole edilen toplam 315 adet izolat incelenmiştir. Demografik ve laboratuvar verileri hastane otomasyon sisteminden retrospektif olarak analiz edilmiştir. Bakteriyel izolatların tanımlanması ve antibiyotik duyarlılığı Vitek 2 Compact (Biomerieux, Fransa) cihazı ile yapılmış ve EUCAST (European Committee on Antimicrobial Susceptibility Testing) kriterlerine göre değerlendirilmiştir. Bulgular: COVID-19 nedeni ile hastanemizde yatan 5.753 hasta incelenmiş ve bunlardan YBÜ’de bulunan 315’inde (%5.5) sekonder bakteriyel enfeksiyon belirlenmiştir. Pandemi döneminde Gram-negatif bakterilerden en çok sırayla Acinetobacter baumannii (%47.8), Klebsiella pneumoniae (%13.4) ve Pseudomonas aeruginosa (%12.0) üremesi görülmüştür. Gram-pozitif bakteriler arasında en çok sırayla Staphylococcus aureus (%4.5) ve Enterococcus spp. (%2.1) bakterileri üremiştir. Sonuç: Çoklu ilaca dirençli bakteriler, morbidite ve mortalitenin artmasına neden olur. Bu nedenle antibiyotik tedavisine duyulan gereksinim çabucak değerlendirilmeli ve uygun olmadığında kesilmelidir. Nozokomiyal enfeksiyonların uygun kontrolünün sağlanması ile COVID-19 hastalarında sekonder bakteriyel enfeksiyon gelişiminin önlenmesi ve bu dirençli türlerin yayılmasını sınırlamak önemlidir.Öğe COVID-19-associated pulmonary aspergillosis (CAPA): identification of Aspergillus species and determination of antifungal susceptibility profiles(Springer, 2023) Ozturk, Ali; Bozok, Taylan; Erdogan, Merve; Ibrahim, Bashar M. S.; Bozok, Tugce SimsekAmong the co-infectious agents in COVID-19 patients, Aspergillus species cause invasive pulmonary aspergillosis (IPA). IPA is difficult to diagnose and is associated with high morbidity and mortality. This study is aimed at identifying Aspergillus spp. from sputum and tracheal aspirate (TA) samples of COVID-19 patients and at determining their antifungal susceptibility profiles. A total of 50 patients with COVID-19 hospitalized in their intensive care units (ICU) were included in the study. Identification of Aspergillus isolates was performed by phenotypic and molecular methods. ECMM/ISHAM consensus criteria were used for IPA case definitions. The antifungal susceptibility profiles of isolates were determined by the microdilution method. Aspergillus spp. was detected in 35 (70%) of the clinical samples. Among the Aspergillus spp., 20 (57.1%) A. fumigatus, six (17.1%) A. flavus, four (11.4%) A. niger, three (8.6%) A. terreus, and two (5.7%) A. welwitschiae were identified. In general, Aspergillus isolates were susceptible to the tested antifungal agents. In the study, nine patients were diagnosed with possible IPA, 11 patients were diagnosed with probable IPA, and 15 patients were diagnosed with Aspergillus colonization according to the used algorithms. Serum galactomannan antigen positivity was found in 11 of the patients diagnosed with IPA. Our results provide data on the incidence of IPA, identification of Aspergillus spp., and its susceptibility profiles in critically ill COVID-19 patients. Prospective studies are needed for a faster diagnosis or antifungal prophylaxis to manage the poor prognosis of IPA and reduce the risk of mortality.Öğe EVALUATION OF AMINO ACID PROFILE IN SERUM OF PATIENTS WITH COVID-19 FOR PROVIDING A NEW TREATMENT STRATEGY(Soc Medical Biochemists Serbia, 2022) Ozturkl, Ali; Bayraktar, Nihayet; Bayraktar, Mustafa; Ibrahim, Bashar; Bozok, Taylan; Ceylan, Mehmet ResatBackgroundAmino acids have an important role in metabolism and may affect COVID-19-related outcomes. In our study, the amino acid serum level of hospitalized COVID19 patients was evaluated to determine a new treatment strategy.MethodsThe amino acid profile covering 43 amino acids in 68 subjects, comprising 30 (14 men and 16 women) controls and 38 (16 men and 22 women) COVID-19 patients, were examined. The amino acid profiles of the participants were screened by LC-MS/MS.ResultsCompared with the control group, serum levels of 27 amino acids increased in the patient group. Alpha-aminopimelic acid, sarcosine, and hydroxyproline amino acids were considerably higher in the control group than in the patient group (p<0.0001). There was no notable difference among control group and the case group for 13 amino acids (p >= 0.05). A significant positive correlation was seen among the control and the patient groups in the mean amino acid values (r=0.937; p<0.0001).ConclusionsThese results postulated a clear picture on the serum levels of amino acid in the COVID-19 patients. Serum amino acids measured in hospitalized COVID-19 patients can explain the patient's metabolic status during the disease.Öğe Evaluation of rapid antibody test and chest computed tomography results of COVID-19 patients: A retrospective study(Wiley, 2021) Ozturk, Ali; Bozok, Taylan; Simsek Bozok, TugceThe purpose of this study was to evaluate the SARS-CoV-2 immunoglobulin M/immunoglobulin G (IgM/IgG) rapid antibody test results in symptomatic patients with COVID-19 and their chest computed tomography (CT) data. A total of 320 patients admitted to our hospital for different durations due to COVID-19 were included in the study. Serum samples were obtained within 0-7 days from COVID-19 patients confirmed by reverse-transcription polymerase chain reaction (RT-PCR) and chest CT scan. According to the SARS-CoV-2 RT-PCR results, the patients included in the study were divided into two groups: PCR positive group (n = 46) and PCR negative group (n = 274). The relationship between chest CT and rapid antibody test results were compared statistically. Of the 320 COVID-19 serum samples, IgM, IgG, and IgM/IgG were detected in 8.4%, 0.3%, and 11.6% within 1 week, respectively. IgG/IgM antibodies were not detected in 79.7% of the patients. In the study, 249 (77.8%) of 320 patients had positive chest CT scans. Four (5.6%) of 71 patients with negative chest CT scans had IgM and two (2.8%) were both IgM/IgG positive. IgM was detected in 23 (9.2%), IgG in one (0.4%), and IgM/IgG in 35 (14%) of chest CT scan positive patients. The rate of CT findings in patients with antibody positivity was found to be significantly higher than those with antibody negativity. The results of the present study show the accurate and equivalent performance of serological antibody assays and chest CT in detecting SARS-CoV-2 within 0-7 days from the onset of COVID19 symptoms. When RT-PCR is not available, we believe that the combination of immunochromatographic test and chest CT scan can increase diagnostic sensitivity for COVID-19.Öğe Üçüncü basamak bir hastanede rotavirüs, enterik adenovirüs veenterik parazit enfeksiyonlarının prevalansı ve demografiközellikleri: Altı yıllık retrospektif kesitsel çalışma(2021) Bozok, Taylan; Bozok, Tuğçe ŞimşekAmaç: Bu çalışmada ishal ön tanılı hastaların rotavirüs, enterik adenovirüs ve enterik parazit inceleme sonuçlarının demografik verilerle ilişkilerinin analiz edilmesi amaçlandı. Yöntem: Ocak 2014 – Aralık 2019 tarihleri arasında Niğde Eğitim ve Araştırma Hastanesi laboratuvarında taze dışkı örneğinde immünkromatografik yöntemle çalışılmış rotavirüs, adenovirüs antijeni ve ışık mikroskobu altında 40x büyütmede parazit inceleme sonuçları retrospektif olarak değerlendirildi. Test sonuçları yaşa, cinsiyete, uyruğa, mevsimlere, yıllara ve hastaneye başvuru şekline göre ki-kare yöntemi ile analiz edildi. p değeri <0.05 istatistiksel olarak anlamlı kabul edildi. Bulgular: İncelenen altı yıllık rotavirüs, adenovirüs ve dışkıda parazit inceleme testlerinin pozitiflik oranları; rotavirüs için %7.7, adenovirüs için %2.3 ve parazit inceleme için %16.8 olarak bulundu. Rotavirüs ve adenovirüs pozitifliği en yüksek 0-2 yaş grubunda (%11.1), parazit görülme oranları ise en yüksek 6-10 yaş grubunda (%23.9) tespit edildi. Rotavirüs pozitifliği kış aylarında, parazit görülme oranları ise yaz aylarında yüksek bulundu (p<0.001). Adenovirüs pozitifliği ise sonbahar ve kış aylarında yüksek oranda tespit edildi (p=0.009). Rotavirüs pozitifliği göçmenlerde daha yüksek oranda tespit edildi (p=0.021). Rotavirüs ve adenovirüs pozitifliği yatan hastalarda, gaitada parazit görülme oranları ayaktan başvuran hastalarda yüksek bulundu (p<0.001). Sonuç:Bölgemizde klinik tanı açısından rotavirüs ve adenovirüse bağlı gastroenteritlerin özellikle kış aylarında ve beş yaş ve altı çocuklarda daha fazla görüldüğü, bunun yanında parazitlere bağlı gastroenteritlerin de yaz aylarında ve 6-10 yaş arası çocuklarda daha sık rastlandığı göz önünde bulundurulmalıdır.
