Person: İLKİ, ZEYNEP ARZU
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İLKİ
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ZEYNEP ARZU
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Publication Open Access Healthcare-associated staphylococcus aureus infections in children in Turkey: A six-year retrospective, single-center study(2023-08-01) İLKİ, ZEYNEP ARZU; KEPENEKLİ KADAYİFCİ, EDA; Yakut N., Ergenç Z., Tuncay S. A., Bayraktar S., Sayın E., İlki Z. A., Kepenekli Kadayifci E.Objective: To describe clinical and epidemiological characteristics, antimicrobial susceptibility and mortality-associated factors of healthcare-associated infections (HCAIs) caused by Staphylococcus (S.) aureus in children. Methods: We conducted a retrospective, single-centre study of pediatric HCAIs caused by S. aureus from a tertiary care hospital in Turkey between February 2014 and December 2019. The clinical and epidemiological characteristics and antimicrobial susceptibility of the methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA) isolates was evaluated. Results: A total of 310 pediatric patients were examined. Overall, 225 (72.6%) isolates were MSSA and 85 (27.4%) were MRSA. All S. aureus isolates were susceptible to teicoplanin, vancomycin, linezolid, tigecycline, mupirocin, and daptomycin. Penicillin resistance rates were high (89.0%), while fosfomycin, gentamicin, and clindamycin resistance rates were low (1.3%, 1.0%, and 2.3%, respectively). Except susceptibility to fosfomycin, which was significantly lower in 2014 compared to 2018 and 2019, no significant difference was found in the antimicrobial susceptibility of S. aureus isolates between the years. Baseline characteristics and mortality rate were similar comparing MRSA and MSSA causing HCAIs. The mortality rate of HCAIs caused by S. aureus was 6.5% (20 patients). Malignancy was an independent risk factor associated with mortality in the multivariate analysis (OR 5.446, 95% CI 1.573- 18.849). Conclusions: Our findings demonstrate that MSSA remained the most causative agent of HCAIs caused by S. aureus. The mortality rate was 6.5%, the antibiotic resistance rate was quite high for penicillin and diagnosis of malignancy was the main risk factor for increasing mortality in children. These findings could help improve the management of HCAIs caused by S. aureus in children.Publication Open Access Atypical Cell'' Parameter in Automated Urine Analysis for the Diagnosis of Bladder Cancer: A Retrospective Pilot Study(GALENOS YAYINCILIK, 2020-04-01) FİLİNTE, DENİZ; Tinay, Ilker; Sahin, Bahadir; Saracoglu, Sertac; Yanilmaz, Ozgur; Aksu, Mehmet Burak; Ayas, Ramazan; Filinte, Deniz; Cam, Haydar Kamil; Ilki, ArzuObjective: To evaluate the application of an automated urine analyzer (AUA) for the diagnosis of bladder cancer (BC) Materials and Methods: A retrospective data analysis of 2365 urine specimens from the department of urology has been performed and matched with those patients, who have undergone cystoscopic evaluation or surgical treatment for different urological pathologies during 2018. After matching, clinical records of the patients has been further evaluated in order to select patients with recent or previous BC diagnosis. To assess the diagnostic efficacy of AUA, patients were divided into five groups according to the patient history of BC and healthy controls. Results: A total of 106 patients are included in this study and the majority (69.8%) of the patients are follow-up patients with previous diagnosis and treatment of non-muscle invasive BC (NMIBC). For patients with low-risk NMIBC (n=27), the sensitivity and specificity were calculated as 75% and 100%. For patients with high-risk NMIBC (n=47), who were previously treated with intravesical BCG, the sensitivity and specificity were calculated as 54.5% and 83.3%. All patients in radical cystectomy group (n=7) with muscle invasive BC had positive urine analyses results for atypical cells. And none of the patients in the control group (n=8) had positive AUA results and cystoscopic evaluation also did not show any bladder mass suspicious for BC. Conclusion: The results of this retrospective pilot study showed acceptable sensitivity and specificity rates of the fluorescence flow cytometry based AUA and the results of the low-risk group are especially valuable regarding its potential use to decide on performing a follow-up cystoscopy or not. A prospective study is currently on progress to validate the findings of the current study.Publication Open Access Performance of Sysmex UF-5000 for candiduria screening(2022-12-01) İLKİ, ZEYNEP ARZU; Yanılmaz Ö., Akşit İlki A.In this study, we tested the performance of the Sysmex UF-5000 system to detect yeast-like cell (YLC) counting to screen for candiduria. Urine samples were screened for leukocyte and yeast amount by flow cytometry and results were compared with fungal culture results. A total of 56,749 urine samples were enrolled in this study. Urine culture and urinalysis of YLC data were used to evaluate the performance of YLC in diagnosing candiduria. Different cut-off values (YLC. 5, 10, 20, 50, 100/µl) were evaluated. Youden index was used to determine the ideal cut-off value, and the highest was 0.95 with 5 YLC/µl. When the cut-off value for YLC is 5 cells/µl, 95.15% of the samples were “negative” with flow cytometry and culture (NPV:100%). In conclusion, detection of YLC by flow cytometer (Sysmex UF-5000) can be a rapid alternative method to exclude candiduria prior to urine culture.Publication Open Access Microbiology of sinusitis and the predictive value of throat culture for the aetiology of sinusitis(ELSEVIER SCI LTD, 2005-05) ÜLGER, NURVER; Ilki, A; Ulger, N; Inanli, S; Ozer, E; Arikan, C; Bakir, M; Soyletir, GA prospective study of throat cultures and maxillary sinus aspirates from children with chronic sinusitis (n = 21), acute sinusitis (n = 28) or a clinical diagnosis of chronic adenoiditis (n = 41) was performed. Seventy-two bacterial pathogens were isolated from sinus aspirates from 52% of the study population. Haemophilus influenzae was most common pathogen, followed by Moraxella catarrhalis, Streptococcus pneumoniae, Staphylococcus aureus, and group A streptococci. Quantitative throat cultures had positive predictive values of 41%, 53% and 75% for H. influenzae, Strep. pneumoniae and M. catarrhalis, respectively, while negative predictive values were 93-98%, indicating that these three pathogens do not cause sinusitis when absent from the throat.Publication Open Access Healthcare-associated Staphylococcus aureus infections in children in Turkey: A six-year retrospective, single-center study(2023-08-01) SAYIN, ELVAN; İLKİ, ZEYNEP ARZU; KEPENEKLİ KADAYİFCİ, EDA; Yakut N., Ergenc Z., Aslan Tuncay S., Bayraktar S., Sayin E., Ilki Z. A., Kepenekli Kadayifci E.Objective: To describe clinical and epidemiological characteristics, antimicrobial susceptibility and mortality-associated factors of healthcare-associated infections (HCAIs) caused by Staphylococcus (S.) aureus in children. Methods: We conducted a retrospective, single-centre study of pediatric HCAIs caused by S. aureus from a tertiary care hospital in Turkey between February 2014 and December 2019. The clinical and epidemiological characteristics and antimicrobial susceptibility of the methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA) isolates was evaluated. Results: A total of 310 pediatric patients were examined. Overall, 225 (72.6%) isolates were MSSA and 85 (27.4%) were MRSA. All S. aureus isolates were susceptible to teicoplanin, vancomycin, linezolid, tigecycline, mupirocin, and daptomycin. Penicillin resistance rates were high (89.0%), while fosfomycin, gentamicin, and clindamycin resistance rates were low (1.3%, 1.0%, and 2.3%, respectively). Except susceptibility to fosfomycin, which was significantly lower in 2014 compared to 2018 and 2019, no significant difference was found in the antimicrobial susceptibility of S. aureus isolates between the years. Baseline characteristics and mortality rate were similar comparing MRSA and MSSA causing HCAIs. The mortality rate of HCAIs caused by S. aureus was 6.5% (20 patients). Malignancy was an independent risk factor associated with mortality in the multivariate analysis (OR 5.446, 95% CI 1.573- 18.849). Conclusions: Our findings demonstrate that MSSA remained the most causative agent of HCAIs caused by S. aureus. The mortality rate was 6.5%, the antibiotic resistance rate was quite high for penicillin and diagnosis of malignancy was the main risk factor for increasing mortality in children. These findings could help improve the management of HCAIs caused by S. aureus in children.Publication Open Access An alternative for urine cultures: Direct identification of uropathogens from urine by MALDI-TOF MS(AKADEMIAI KIADO ZRT, 2020-10-21) ALTINKANAT GELMEZ, GÜLŞEN; Ilki, Arzu Aksit; Ozsoy, Sevim; Gelmez, Gulsen; Aksu, Burak; Soyletir, GunerUrinary tract infections are one of the most common bacterial infections and rapid diagnosis of the infection is essential for appropriate antibiotic therapy. The goal of our study was to identify urinary pathogens directly by MALDI-TOF MS and to perform antibiotic susceptibility tests in order to shorten the period spent for culturing. Urine samples submitted for culture to the Clinical Microbiology Laboratory were enrolled in this study. Urine samples were screened for leukocyte and bacteria amount by flow cytometry. Samples with bacterial load of 10(6)-10(7)/mL were tested directly by MALDI-TOF MS and antibiotic susceptibility tests (AST) were performed. In total, 538 positive urine samples were evaluated in our study. MALDI-TOF MS identified the microorganism directly from the urine sample in 91.8% of these samples and the concordance rate of conventional identification and direct detection was 95.8% for Gram-negatives at the genus and species level. Escherichia coli (n:401) was the most frequently isolated microorganism, followed by Klebsiella pneumoniae (n:57). AST results were generated for 111 of these urine samples and the concordance was 90% and 87% for E. coli and K. pneumoniae, respectively. Our results showed that screening of urine samples with flow cytometry to detect positive samples and identification of uropathogens directly by MALDI-TOF MS with an accuracy of over 90% can be a suitable method particularly for Gram-negative bacteria in clinical microbiology laboratories.Publication Open Access Clinical and immunological outcomes of SARS-CoV-2 infection in patients with inborn errors of immunity receiving different brands and doses of COVID-19 vaccines(2023-09-01) İLKİ, ZEYNEP ARZU; Karabiber E., Atik Ö., Tepetam F. M., Ergan B., İlki A., Karakoç Aydıner E., Özen A., Özyer F., Barış S.Introduction: Vaccines against severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) provide successful control of the coronavirus-2019 (COVID-19) pandemic. The safety and immunogenicity studies are encouraging in patients with inborn errors of immunity (IEI); however, data about mortality outcomes and severe disease after vaccination still need to be fully addressed. Therefore, we aimed to determine the clinical and immunological outcomes of SARS-CoV-2 infection in patients with IEI who have received vaccination. Materials and Methods: Eighty-eight patients with a broad range of molecular etiologies were studied; 45 experienced SARS-CoV-2 infection. Infection outcomes were analyzed in terms of genetic etiology, background clinical characteristics, and immunization history, including the type and number of doses received and the time elapsed since vaccination. In addition, anti-SARS-CoV-2 antibodies were quantified using electrochemiluminescent immunoassay. Results: Patients were immunized using one of the three regimens: inactivated (Sinovac, Coronavac®), mRNA (BNT162b2, Comirnaty®, Pfizer-Biontech), and a combination. All three regimens induced comparable anti-SARS-CoV-2 IgG levels, with no differences in the adverse events. Among 45 patients with COVID-19, 26 received a full course of vaccination, while 19 were vaccine-naive or received incomplete dosing. No patients died due to COVID-19 infection. The fully immunized group had a lower hospitalization rate (23% vs. 31.5%) and a shorter symptomatic phase than the others. Among the fully vaccinated patients, serum IgM and E levels were significantly lower in hospitalized patients than non-hospitalized patients. Conclusion: COVID-19 vaccines were well-tolerated by the IEI patients, and a full course of immunization was associated with lower hospitalization rates and a shorter duration of COVID-19 symptoms.Publication Open Access Detection of vancomycin-resistant enterococci (VRE) in stool specimens submitted for Clostridium difficile toxin testing(SOC BRASILEIRA MICROBIOLOGIA, 2017-07) İLKİ, ZEYNEP ARZU; Ozsoy, Sevim; Ilki, ArzuThe aim of this study was to determine the association between Clostridium difficile (C. difficile) and vancomycin-resistant Enterococcus (VRE) and efficacy of screening stools submitted for C. difficile toxin assay for prevalence of VRE. Between April 2012 and February 2014, 158 stool samples submitted for C. difficile toxin to the Marmara University Microbiology Laboratory, were included in the study. Stool samples were analyzed by enzyme immuno assay test; VIDAS (bioMerieux, France) for Toxin A&B. Samples were inoculated on chromID VRE (bioMerieux, France) and incubated 24 h at 37 degrees C. Manuel tests and API20 STREP (bioMerieux, France) test were used to identify the Enterococci species. After the species identification, vancomycin and teicoplanin MIC's were performed by E test and molecular resistance genes for vanA vs vanB were detected by polymerase chain reaction (PCR). Of the 158 stool samples, 88 were toxin positive. The prevalence of VRE was 17%(n:19) in toxin positives however, 11.4% in toxin negatives(n:70). All VRE isolates were identified as Enterococcus faecium. These results were evaluated according to Fischer's exact chi-square test and p value between VRE colonization and C. difficile toxin positivity was detected 0.047 (p < 0.05). PPV and NPV were 79% and 47% respectively. In our study, the presence of VRE in C. difficile toxin positives is statistically significant compared with toxin negatives (p < 0.05). Screening for VRE is both additional cost and work load for the laboratories. Therefore VRE screening among C. difficile toxin positive samples, will be cost effective for determination of high risk patients in the hospitals especially for developing countries (C) 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda.Publication Open Access Prevalence of Norovirus Coinfection in Clostridioides difficile Toxin Positive Patients(2024-09-01) SAYIN, ELVAN; İLKİ, ZEYNEP ARZU; Şalcı Aslan H. Ş., Akıllı F. M., Sayın E., İlki Z. A.Objective: In this study we aimed to evaluate the prevalence of norovirus genogroups I and II and C.difficile coinfection among patients with gastroenteritis symptoms. Method: A total of 76 patients with diarrhea were included in the study. Of these, 40 are children (<18y), 23 are adults between the ages of 18-65y, and 13 are patients older than 65 years. All these were C.difficile toxin GDH/Toxin A+B (BIOTEC, Spain) positive. In these toxin positive stool samples, Norovirus GI and GII antigen was studied by 2 methods; i.ELISA (R Biopharm, Darmstadt, Germany) and ii.polymerase chain reaction (RT – PCR). We compared the results of the antigen test (ELISA) with those of PCR for the detection of norovirus in stool specimens. SPSS 19.0 statistical program was used to evaluate the data of the research. Results: Out of 76 stool samples tested, 3 (3.9%) were positive for norovirus by ELISA. Subsequent RT-PCR identified norovirus GI and GII in 7 samples (9.2%). Concerning RT-PCR, the sensitivity of the ELISA test was 42.8%, and the specificity was found as 96%. Conclusion: The study identified a 9.2% rate of co-infection with C. difficile and norovirus, with this co-infection being particularly prevalent in children. This finding emphasizes the critical need to consider both co-infection and C. difficile infection as potential causes of diarrhea in hospitalized patients, especially those under 18 or over 65 years old. Keywords: C. difficile, Coinfection, ELISA, Norovirus, PCR