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Öğe The antimicrobial effects of ketamine combined with propofol: An in vitro study(Elsevier Science Inc, 2013) Begec, Zekine; Yucel, Aytac; Yakupogullari, Yusuf; Erdogan, Mehmet Ali; Duman, Yucel; Durmus, Mahmut; Ersoy, M. OzcanBackground and objectives: Ketamine and propofol are the general anesthetics that also have antimicrobial and microbial growth-promoting effects, respectively. Although these agents are frequently applied together during clinical use, there is no data about their total effect on microbial growth when combined. In this study, we investigated some organisms' growth in a ketamine and propofol mixture. Method: We used standard strains including Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans in this study. Time-growth analysis was performed to assess microbial growth rates in 1% propofol. Antimicrobial activity of ketamine, alone and in propofol was studied with microdilution method. Results: In propofol, studied strains grew from 103-104 cfu/mL to ?AO cfu/mL concentrations within 8-16 hours depending on the type of organism. Minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) (for candida, minimal fungicidal concentration) of ketamine were determined as follows (MIC, MBC): E.coli 312.5, 312.5 pg/mL; S.aureus 19.5, 156 pg/mL; P.aeruginosa 312.5, 625 pg/mL; and C.albicans 156, 156 pg/ml. In ketamine+propofol mixture, ketamine exhibited antimicrobial activity to E.coli, P.aeruginosa and C.albicans as MBCs at 1250, 625 and 625 pg/mL, respectively. Growth of S. aureus was not inhibited in this mixture (ketamine concentration=1250 pg/mL). Conclusion: Ketamine has sustained its antimicrobial activity in a dose-dependent manner against some organisms in propofol, which is a strong microbial growth-promoting solution. Combined use of ketamine and propofol in routine clinical application may reduce the risk of infection caused by accidental contamination. However, one must keep in mind that ketamine cannot reduce all pathogenic threats in propofol mixture. (C) 2013 Sociedade Brasileira de Anestesiologia. Published by Elsevier Editora Ltda. All rights reserved.Öğe A Case of Tubo-ovarian Abscess due to Salmonella enterica Following an In Vitro Fertilization Attempt(Galenos Yayincilik, 2019) Yakupogullari, Yusuf; Isik, Burak; Gursoy, Nafia Canan; Bayindir, Yasar; Otlu, Baris[Abstract Not Available]Öğe Clinical Characteristics and Outcomes of Liver Transplantation Recipients With COVID-19 Pneumonia(Elsevier Science Inc, 2021) Kose, Adem; Toplu, Sibel Altunisik; Yalcinsoy, Murat; Yakupogullari, Yusuf; Otlu, Baris; Otan, Emrah; Aydin, CemalettinBackground. We aimed to evaluate the clinical characteristics and outcomes of mild-severe COVID-19 pneumonia cases in liver transplant (LT) recipients. Methods. Ten LT recipients diagnosed as having COVID-19 pneumonia in a 6-month period in our transplantation center were included. Demographic and medical data of the recipients were retrospectively collected; clinical courses, treatment responses, and outcomes were evaluated. Results. Ten LT recipients were male, had a median age of 57 years (min-max, 36-69 years; interquartile range [IQR], 13 years), and had right lobe from living donor LT performed in a median of 11 months (min-max, 1-72 months; IQR, 12 months). Five patients had severe pneumonia, and the remaining patients had mild/moderate pneumonia. The most frequent symptoms were fever (90%) and cough (70%). Favipiravir, enoxaparin sodium, and corticosteroid were initiated at the time of the diagnosis; immunosuppressive drug doses were reduced or discontinued in 3 cases. Lymphopenia median: 510/mL (min-max, 90-1400 mL; IQR, 610 mL), increased levels of C-reactive protein median: 4.72 (min-max, 0.31-23.4; IQR, 8.5), and ferritin median: 641 (min-max, 40 to >= 1650; IQR, 1108) were frequent. Four patients required antibacterial treatments because of emerging bacterial pneumonia and/or sepsis. All patients were hospitalized for a median of 10 days. One patient with sepsis died on the 26th day after intensive care unit admission, and the remaining 9 survived. No further complication was recorded for 1-month follow-up. Conclusions. Commencing favipiravir, enoxaparin sodium, and corticosteroid treatments; close follow-up of the developing complications; the temporary reduction or cessation of immunosuppression; a multidisciplinary approach; early awareness of the bacterial infections; and the initiation appropriate antibiotic treatments can contribute to success.Öğe Clinical Properties of COVID-19 Developed in the Patients with Tuberculosis(Ankara Microbiology Soc, 2022) Otlu, Baris; Yakupogullari, Yusuf; Tanriverdi, Elif Seren; Bentli, RecepThere are limited publications about the Coronavirus disease 19 (COVID-19) clinic developing in the patients with active tuberculosis (TB). In this study, it was aimed to determine some clinical features of patients diagnosed with TB who also had COVID-19. In this retrospective cross-sectional study, 71 pa- tients with COVID-19 were evaluated out of a total of 595 patients diagnosed with TB in our province between 2015 and 2021. After contracting COVID-19, a total of nine (12.6%) TB patients were hospital- ized, five (7%) patients were admitted to the intensive care unit, three (4.2%) were intubated, and one (1.4%) died due to severe COVID-19. The frequency of such health problems was found to be higher than the normal population living in the same province. None of these complications were observed in a total of 40 female TB patients, and the hospital and intensive care unit admission rates for men were significantly higher than for women. The results of this study showed that men with active TB had more health problems due to COVID-19 than the normal population. Comprehensive studies are needed to detail the resilience of female TB patients against COVID-19.Öğe Contact-lens-related corneal ulcer caused by klebsiella pneumoniae(Hospital Clinicas, Univ Sao Paulo, 2011) Cumurcu, Tongabay; Firat, Pembegul; Ozsoy, Ercan; Cavdar, Mufide; Yakupogullari, Yusuf[Abstract Not Available]Öğe Development of nucleic acid based lateral flow assays for SARS-CoV-2 detection(Soc Bioscience Bioengineering Japan, 2023) Derin, Dilek Cam; Gultekin, Enes; Taskin, Irmak Icen; Yakupogullari, YusufSARS-CoV-2 is still threat for humanity and its detection is crucial. Although real time reverse transcriptase poly-merase chain reaction is the most reliable method for detection of N protein genes, alternative methods for molecular detection are still needed. Thus, lateral flow assay models for 2019-nCoV_ N3 were developed for molecular detection. Briefly, gold nanoparticles were used as label and three sandwich models (1A, 1B, and 1.2) were designed. Prob con-centrations on gold nanoparticles, types of sandwich model and membrane, limit of detection of target gene and buffer efficiency were studied. Model 1B has shown the best results with M170 membrane. Lower limit of detection was achieved by model 1.2 as 5 pM. All parameters have significant role for molecular detection of SARS-CoV-2 by lateral flow assays, and these results will be useful for nucleic acid based lateral flow assays for viral detection or multiple detection of mutated forms in various detection systems.(c) 2022, The Society for Biotechnology, Japan. All rights reserved.Öğe Diagnostic and treatment outcomes of patients with pulmonary tuberculosis in the first year of COVID-19 pandemic(Who Eastern Mediterranean Regional Office, 2022) Yakupogullari, Yusuf; Ermis, Hilal; Kazgan, Zeynep; Otlu, Baris; Bayindir, Yasar; Gulbas, Gazi; Tanriverdi, ElifBackground: The COVID-19 pandemic has put a significant strain on human life and health care systems, however, little is known about its impact on tuberculosis (TB) patients. Aims: To assess the impact of COVID-19 pandemic on pulmonary tuberculosis (PTB) diagnosis, treatment and patient outcomes, using the WHO definitions. Methods: A cross-sectional study was conducted in Malatya region, Turkey (population 800 000). Data on regional PTB test numbers, case notification rates and PTB patients' clinical characteristics and treatment outcomes were collected. Data from the first pandemic year (2020) were compared to data from the previous 3 years (2017-2019). The attitudes and experiences of patients were analysed. Results: Despite a non-significant 22% decrease in annual PTB case notifications (P = 0.317), the number of TB tests performed (P = 0.001) and PTB patients evaluated (P = 0.001) decreased significantly during the pandemic year compared with the previous 3 years. The proportion of patients with high (3/4+) sputum acid-fast bacilli grades (P = 0.001), TB relapse (P = 0.022) and treatment failure (P = 0.018) increased significantly. The median 64.5-day treatment delay detected in 2017-2019 increased significantly to 113.5 days in 2020 (P = 0.001), due primarily to patients' reluctance to visit a health care facility. Conclusion: In addition to the problems with case detection, this study shows notable deterioration in several indicators related to the severity, contagiousness and poor outcomes of TB, which had already been suppressed for decades.Öğe Differential diagnosis of the granulomatous appendicitis: Retrospective analysis of 16 cases(Turkish Assoc Trauma Emergency Surgery, 2021) Akbulut, Sami; Koc, Cemalettin; Sarici, Kemal Baris; Samdanci, Emine; Yakupogullari, Yusuf; Bayindir, YasarBACKGROUND: This study aims to present the usability of real-time polymerase chain reaction (PCR) and interferon-gamma release assay (IGRA) in the differential diagnosis of granulomatous appendicitis (GAp), especially in areas where tuberculosis (TB) is endemic. METHODS: Sixteen patients underwent appendectomy with presumed diagnosis of acute appendicitis were retrospectively analyzed for histopathological diagnosis of GAp. Real-time PCR method was used to show the whether presence of DNA of the tubercle bacilli in paraffin-embedded tissue blocks. IGRA test was used to investigate whether tubercle bacilli-specific interferon gamma was present in peripheral blood. RESULTS: Sixteen patients (male: 10 female: 6) aged between 21 and 82 years were included in this study. All patients had acute appendicitis and three of them also had appendiceal perforation. Histopathologically, necrotizing granulomatous inflammation was detected in all appendectomy specimens. Acid-fast bacilli were not detected in any of the pathology slides stained with Ehrlich-Ziehl-Neelsen. Real-time PCR was studied in paraffin-embedded tissue blocks of all patients with GAp, but the TB bacilli DNA was amplified in only three patients. IGRA test was studied in peripheral blood samples of 12 patients with GAp and results were as follows: negative (n=9), positive (n=2) and indeterminate (n=1). CONCLUSION: We believe that the use of anamnesis, histopathological findings, tissue PCR, blood IGRA and clinical findings together are important for differential diagnosis of GAp, especially where TB is endemic. We also suggest that all appendectomy specimens should be sent to the laboratory for histopathological evaluation even if specimens appear macroscopically normal.Öğe Do mobile phones of patients, companions and visitors carry multidrug-resistant hospital pathogens?(Mosby-Elsevier, 2011) Tekerekoglu, Mehmet Sait; Duman, Yucel; Serindag, Ayfer; Cuglan, Serpil Semiha; Kaysadu, Halim; Tunc, Emine; Yakupogullari, YusufA cross-sectional study was conducted to determine bacterial colonization on the mobile phones (MPs) used by patients, patients' companions, visitors, and health care workers (HCWs). Significantly higher rates of pathogens (39.6% vs 20.6%, respectively; P = .02) were found in MPs of patients' (n = 48) versus the HCWs' (n = 12). There were also more multidrug pathogens in the patents' MPs including methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase-producing Escherichia coli, and Klebsiella spp, high-level aminoglycoside-resistant Enterococcus spp, and carabepenem-resistant Acinetobacter baumanii. Our findings suggest that mobile phones of patients, patients' companions, and visitors represent higher risk for nosocomial pathogen colonization than those of HCWs. Specific infection control measures may be required for this threat.Öğe The Effect of Chronic Alcoholism on the Conjunctival Flora(Taylor & Francis Inc, 2016) Gunduz, Goksel; Gunduz, Abuzer; Polat, Nihat; Cumurcu, Birgul Elbozan; Yakupogullari, YusufAim: We aimed to investigate the effect of alcohol abuse on the conjunctival flora.Materials and methods: The cases were evaluated as two groups. The study group consisted of 55 heavy-drinking males diagnosed with alcohol abuse, while the control group consisted of 55 males without a history of alcohol abuse. Samples were taken from the inferior fornix conjunctiva with sterile cotton-tipped swabs (Amies transport medium) for culture. The samples were inoculated into blood agar, chocolate agar, eosine methylene blue agar and Saboraud-Dextrose agar (Oxoid/UK) with the dilution method.Results: The microorganisms that grew in study group subjects were Coagulase Negative Staphylococcus (CNS) in 30 (54.5%), Staphylococcus aureus in 14 (25.5%), Moraxella spp. in 3 (5.5%), Streptococcus spp. in 3 (5.5), Bacillus spp. in 3 (5.5%), Corynebacterium spp. in 3 (5.5%), Candida spp. in 3 (5.5%), Haemophilus spp. in 2 (3.6%), Acinetobacter spp. in 2 (3.6%), Neisseria spp. in 1 (1.8%) and Micrococcus spp. in 1 (1.8%). The results for control group were CNS in 31 (56.4%), Bacillus spp. in 7 (12.7%), S. aureus in 5 (9.1%), and Corynebacterium spp. in 2 (3.6%). Moraxella spp., Streptococcus spp., Candida spp., Haemophilus spp., Acinetobacter spp., Neisseria spp. and Micrococcus spp. microorganisms grew in the conjunctival flora samples of the study group but not in the control group. S. aureus colonization was significantly higher in the study group than the control group (p<0.05).Conclusion: The S. aureus colonization rate was statistically significantly higher in the study group. Some microorganisms only grew in the conjunctival flora samples of the study group. These findings indicate that the conjunctival flora in persons with chronic alcoholism is different than the normal population.Öğe The Effects of Colistin on Imipenem MICs in OXA-48 Producing Klebsiella pneumoniae Isolates: An In Vitro Study(Galenos Publ House, 2021) Duman, Yucel; Tekerekoglu, Mehmet Sait; Kuzucu, Cigdem; Yakupogullari, YusufIntroduction: A new approach to carbapenem resistance-K. pneumoniae infections is to use combination drug therapies. However, little data are available about the effectiveness of the in vitro carbapenem plus colistin combination against oxacillinase-48 (OXA-48) producing K. pneumoniae. Therefore, the aim of this study is to assess the potential synergistic activity of imipenem plus colistin in OXA-48-producing K. pneumoniae strains and investigate the changes in the imipenem minimal inhibitory concentrations (MICs) to varying MICs of colistin. Materials and Methods: Carbapenem and colistin resistance (CoIR) genes were investigated by polymerase chain reaction. In the first stage, synergistic properties were determined by the checkerboard combination method. In the second step, at varying colistin concentrations, changes in the imipenem MICs were investigated. Results: Colistin MIC50 2 mu g/ml, MIC90 16 mu g/ml, and imipenem MIC50 32 mu g/ml, MIC90 128 mu g/ml were found, respectively. According to the fractional inhibitor concentration (FIC) formula, 62.2% of the isolates were synergistic, and 37.8% were indifference. When the colistin was fixed at 0.125 mu g/ml, 0.25 mu g/ml, 0.5 mu g/ml, 1 mu g/ml, and 2 mu g/ml, respectively. Significant decreases were observed in the imipenem Mies, especially of colistin-sensitive isolates. However, imipenem MICs of CoIR isolates did not decrease to susceptible levels. Conclusion: This information will facilitate the design of antibiotic regimens that are more suitable for treating infections due to such pathogens producing OXA-48 and prolong these antibiotics' efficacy. Further in vitro research is required to determine which treatment combination is best and its optimal use as combination therapy to treat these infections.Öğe The Effects of COVID-19 Infection Control Measures on the Frequency of Rotavirus and Enteric Adenovirus in Children(Aves Yayincilik, Ibrahim Kara, 2022) Duman, Yuecel; Yakupogullari, Yusuf; Gunduz, AytenObjective: The coronavirus disease 2019 pandemic has caused many changes in our lifestyle, such as the flow of our daily lives, communica-tion between individuals, traveling, eating, and drinking habits. These changes have reduced the risk of viral infections. In this study, it was aimed to examine the changes in the frequency of rotavirus and enteric adenovirus in children due to changes in lifestyle such as hand hygiene, physical distance and eating habits in individuals before and during the COVID-19 pandemic.Material and Methods: We analyzed data obtained from the labora-tory electronic records of hospitals in our region to assess the changes of rotavirus and adenovirus frequency and number of patients admit-ted to the hospital during the COVID-19 pandemic period compared to pre-pandemic years. Rotavirus and enteric adenovirus antigens were studied using a qualitative immunochromatographic method.Results: Between January 2018 and July 2021, a total of 68.504 patient samples were tested, 60.513 (88.3%) before the COVID-19 pandemic and 7991 (11.7%) during the pandemic. Mean age of the patients was deter-mined as 4.7 years. Before the pandemic, a total of 6.815 (11.3%) sam-ples for rotavirus and 1.873 (3.1%) samples for adenovirus were found positive. During the pandemic period, a total the 598 (7.5%) samples for rotavirus and 164 (2%) samples for adenovirus were found positive. Monthly median test numbers for rotavirus and adenovirus significant-ly fell about 75% (1.926 vs 493, p< 0.001). In addition, monthly median positivity rates of rotavirus (10.9% vs 7.1%, p= 0.002) and adenovirus (2.9% vs 1.8%, p< 0.001) reduced about 35% and 38%, respectively, after the onset of the pandemic as compared to the pre-pandemic years. The decrease in mean monthly test numbers and the reduction in the frequency of positive samples collectively indicated that the frequencies of both pathogens substantially reduced during the pandemic because of infection control measures.Conclusion: The fact that the COVID-19 pandemic forces us to comply with infection control rules and change our lifestyle shows us that these rules are very important not only in controlling the pandemic, but also in controlling other viral infections.Öğe Emerging Tuberculosis Among Patients with Previous COVID-19(Bilimsel Tip Yayinevi, 2022) Yakupogullari, Yusuf; Tanriverdi, Elif Seren; Ermis, Hilal; Otlu, BarisCOVID-19 patients have a higher incidence of opportunistic infections, but there is little information on tuberculosis (TB). In this study, it was aimed to determine any possible contribution of COVID-19 in TB emergence among patients diagnosed with TB during the pandemic. A retrospective screening of the regional TB laboratory's records identified TB patients diagnosed in the Malatya region between April 1, 2020, and December 31, 2021. Medical data of TB patients with a prior COVID-19 were evaluated. During the study period, 171 TB patients were diagnosed in the region, with 26 also infected with SARS-CoV-2. Patients' histories revealed that 10 (38.5%) of these 26 patients developed TB symptoms in a median 68.5 days after COVID-19. Four patients had one-week to two-month corticosteroid treatment due to severe COVID-19, and one had a hematological malignancy history. However, the remaining five patients had no significant predisposing factor for TB relapse. Four out of 10 patients were free of any finding for active TB before COVID-19. Severe COVID-19 may have some obvious implications for TB reactivation, but there was no conclusive evidence of such an effect in mild to moderate COVID-19. Nonetheless, inquiring about COVID-19 histories from TB patients in large-scale studies may provide high-quality evidence about the interactions between the two pathogens.Öğe Evaluation of diagnostic performance of new antigen-based enzyme immune assay for diagnosis of Hepatitis C virus (HCV) infections(Academic Journals, 2012) Kooglu, Mehmet; Ak, Sibel; Ak, Muharrem; Yakupogullari, Yusuf; Ozer, AliLaboratory diagnosis of Hepatitis C virus (HCV) is sometimes problematic. A novel immune enzyme assay (HCV-Core Antigen, Abbott Laboratories/Germany) has been recently licensed for detection of HCV antigen in human serum. In this study, we aimed to evaluate diagnostic performance of this new test in comparison with the HCV-RNA quantification and anti-HCV antibody (anti-HCV-Ab) analyses. A total of 152 serum samples of which 112 anti-HCV-Ab positive (range 1.08 to 386.54 s/co) and 40 anti-HCV-Ab negative (<1 s/co) were analyzed with HCV-RNA and HCV-Ag tests. According to HCV-RNA detection, sensitivity and specificity of HCV-Ag test was measured as 96.9 and 100%, respectively and of anti-HCV-Ab were measured as 100 and 60%, orderly. An excellent positive predictive value for HCV-Ag test was detected as 100%, whereas 28.5% for anti-HCV-Ab test. Pearson correlation analysis showed that there was a statistically significant and strong relationship (p < 0.001, R: 0.773) between HCV-Ag and HCV-RNA quantification analysis. The correlation between the two tests showed an exponential trend (R-2: 0.949). These results suggest that HCV-Ag test may be a reliable assay for HCV antigen detection, which is also well-correlated with serum viral load. However, large studies, including different HCV genotypes and with extreme viral quantity, are required to assess analytic potency of this novel kit.Öğe An evaluation of patients with a previous endemic coronavirus infection during the COVID-19 pandemic(Wiley, 2021) Otlu, Baris; Yakupogullari, Yusuf; Tanriverdi, Elif S.; Bayindir, YasarFew studies exist on the clinical manifestation of coronavirus disease 2019 (COVID-19) in patients who previously had a common cold due to an endemic coronavirus (eCoV). In a retrospective scan of the data obtained in our microbiology laboratory, 64 patients who were diagnosed with an eCoV infection between 2016 and 2020 were identified. National COVID-19 surveillance data showed that four (6.2%) of 64 patients were infected with severe acute respiratory syndrome coronavirus 2 by the end of 2020, while, simultaneously, the COVID-19 prevalence in the city of Malatya ranged from 7.8% (polymerase chain reaction-based diagnosis) to 9.2% (total diagnosis). The differences were found statistically significant (6.2% vs. 7.8%, p < .01; 6.2% vs. 9.2%, p < .001). Patient interviews and evaluation of medical records revealed that these four patients did not manifest any severe COVID-19 symptoms despite their substantial comorbidities, and they did not require hospitalization. Consequently, despite a low number of samples, we determined a lower frequency of COVID-19 among the patients who had a prior eCoV infection, and the results of this study support the previous findings that people with a prior eCoV infection develop a milder case of COVID-19. Our results may provide some insights for future studies aiming at vaccine development, but detailed investigations are still required.Öğe Evaluation of the Diagnostic Performance of Xpert MTB/RIF Test for the Detection of Mycobacterium tuberculosis and Rifampin Resistance in Clinical Samples(Ankara mıcrobıology soc, hacetlepe unıv faculty medıcıne dept mıcrobıology, 06100 ankara, turkey, 2016) Gursoy, Nafia Canan; Yakupogullari, Yusuf; Tekerekoglu, Mehmet Sait; Otlu, BarisRapid and accurate detection of active tuberculosis (TB) cases is one of the most important goal of tuberculosis control programme. For this purpose, new methods are being developed to isolate, serotype and determine the drug resistance of the agent. Xpert MTB/RIF test (CepheidGeneXpert (R) System, USA) that has been recently developed, is a real-time polymerase chain reaction-based method which detects Mycobacterium tuberculosis complex and resistance of the strain to rifampicin (RIF) from the clinical sample directly within a couple of hours. However, there are not sufficient data about the performance of that test for extrapulmonary samples and pulmonary samples other than sputum. The aims of this study were to investigate the sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF test in detection of M. tuberculosis and the performance in the determination of rifampicin resistance of the isolates from pulmonary and extrapulmonary clinical samples. A total of 2160 clinical samples, in which 1141 (52.8%) were pulmonary and 1019 (47.2%) were extrapulmonary samples, sent to our laboratory between July 2013 to December 2014, were included in the study. Sixty seven of the evaluated samples (3.1%) were positive with microscopy (acid-fast stain; AFS), 116 samples (5.1%) were positive with culture and 98 samples (4.5%) were positive with Xpert MTB/RIF test. When the culture was considered as the reference method, the sensitivity and specificity of Xpert MTB/RIF test were determined as 73.3% and 99.3%, respectively for all samples; 77.5% and 99.5%, respectively for pulmonary samples and 63.9% and 99.2%, respectively for extrapulmonary samples. Among AFS positive samples, the sensitivity was 100% and specificity was 66.7%; whereas among AFS negative samples those values were 40.4% and 99.4%, respectively. Among all the samples involved in the study, RIF resistance was determined only in three samples with Xpert MTB/RIF test and that was also proved phenotypically (100% concordance). According to mycobacterial culture results, positive and negative predictive values of Xpert MTB/RIF test were determined as 86.7% and 98.5%, respectively for all samples. Those were determined as 92.5% and 98.3%, respectively for extrapulmonary samples and were determined as 74.2 and 98.7%, respectively for pulmonary samples. According to the results obtained in our study, sensitivity of Xpert MTB/RIF test for extrapulmonary samples was found to be at moderate level; sensitivity of the test was found to be decreased especially in AFS negative samples with less bacilli load. Nonetheless, specificity of Xpert MTB/RIF test to the agent in all samples was found to be extremely high. In our study, although RIF-resistant strains were detected in few of the samples, Xpert MTB/RIF test could differentiate all resistant and sensitive strains. Additionally, detection of M. tuberculosis and RIF resistance in our laboratory takes approximately 20.96 days with culture, this period decreases to a couple of hours with Xpert MTB/RIF test. Because of the advantages such as being practical, rapid and requiring minimal safety measures, it was concluded that Xpert MTB/RIF test may contribute to rapid diagnosis of TB also in extrapulmonary samples, with the confirmation of culture method.Öğe Evaluation of the Diagnostic Performance of Xpert MTB/RIF Test for the Detection of Mycobacterium tuberculosis and Rifampin Resistance in Clinical Samples(Ankara Microbiology Soc, 2016) Gursoy, Nafia Canan; Yakupogullari, Yusuf; Tekerekoglu, Mehmet Sait; Otlu, BarisRapid and accurate detection of active tuberculosis (TB) cases is one of the most important goal of tuberculosis control programme. For this purpose, new methods are being developed to isolate, serotype and determine the drug resistance of the agent. Xpert MTB/RIF test (CepheidGeneXpert (R) System, USA) that has been recently developed, is a real-time polymerase chain reaction-based method which detects Mycobacterium tuberculosis complex and resistance of the strain to rifampicin (RIF) from the clinical sample directly within a couple of hours. However, there are not sufficient data about the performance of that test for extrapulmonary samples and pulmonary samples other than sputum. The aims of this study were to investigate the sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF test in detection of M. tuberculosis and the performance in the determination of rifampicin resistance of the isolates from pulmonary and extrapulmonary clinical samples. A total of 2160 clinical samples, in which 1141 (52.8%) were pulmonary and 1019 (47.2%) were extrapulmonary samples, sent to our laboratory between July 2013 to December 2014, were included in the study. Sixty seven of the evaluated samples (3.1%) were positive with microscopy (acid-fast stain; AFS), 116 samples (5.1%) were positive with culture and 98 samples (4.5%) were positive with Xpert MTB/RIF test. When the culture was considered as the reference method, the sensitivity and specificity of Xpert MTB/RIF test were determined as 73.3% and 99.3%, respectively for all samples; 77.5% and 99.5%, respectively for pulmonary samples and 63.9% and 99.2%, respectively for extrapulmonary samples. Among AFS positive samples, the sensitivity was 100% and specificity was 66.7%; whereas among AFS negative samples those values were 40.4% and 99.4%, respectively. Among all the samples involved in the study, RIF resistance was determined only in three samples with Xpert MTB/RIF test and that was also proved phenotypically (100% concordance). According to mycobacterial culture results, positive and negative predictive values of Xpert MTB/RIF test were determined as 86.7% and 98.5%, respectively for all samples. Those were determined as 92.5% and 98.3%, respectively for extrapulmonary samples and were determined as 74.2 and 98.7%, respectively for pulmonary samples. According to the results obtained in our study, sensitivity of Xpert MTB/RIF test for extrapulmonary samples was found to be at moderate level; sensitivity of the test was found to be decreased especially in AFS negative samples with less bacilli load. Nonetheless, specificity of Xpert MTB/RIF test to the agent in all samples was found to be extremely high. In our study, although RIF-resistant strains were detected in few of the samples, Xpert MTB/RIF test could differentiate all resistant and sensitive strains. Additionally, detection of M. tuberculosis and RIF resistance in our laboratory takes approximately 20.96 days with culture, this period decreases to a couple of hours with Xpert MTB/RIF test. Because of the advantages such as being practical, rapid and requiring minimal safety measures, it was concluded that Xpert MTB/RIF test may contribute to rapid diagnosis of TB also in extrapulmonary samples, with the confirmation of culture method.Öğe Extended-Spectrum ?-Lactamase-Producing Escherichia coli and Klebsiella spp. in Community-Acquired Urinary Tract Infections and Their Antimicrobial Resistance(Doc Design Informatics Co Ltd, 2020) Senol, Arzu; Yakupogullari, Yusuf; Senol, Feray FerdaObjective: Production of extended-spectrum beta-lactamases (ESBLs) is the most important antimicrobial resistance mechanism among Gram-negative pathogens. In this study, ESBL frequency and antimicrobial resistance of Escherichia coli and Klebsiella spp. isolated from community-acquired urinary tract infections (UTIs) are investigated. Methods: In this retrospective cross-sectional study, ESBL rates and the results of antimicrobial susceptibility tests were determined for E. coli and Klebsiella spp. grown in the urine cultures of 520 patients with community-acquired UTI, and the changes in the antimicrobial resistance rates of the isolates were compared in terms of ESBL production. Results: E. coli had grown in 220 samples and Klebsiella spp. in 38 samples. ESBL production frequencies of the isolates were found as 40% and 47.4%, respectively, and the rate of carbapenem resistance was found as 3.1%. Among the isolates, the highest resistance was found for amoxicillin-clavulanate (46%), ciprofloxacin (44.9%), and ceftriaxone (42.2%), while the lowest resistance was found for colistin (0.3%), fosfomycin (1.5%), amikacin (3.1%), and nitrofurantoin (4.2%). In ESBL-producers, significantly higher resistance was found for all antibiotics studied, except colistin, nitrofurantoin and fosfomycin. Conclusions: In this study, it was shown that almost half of the community-acquired isolates were ESBL-producers, and these isolates had acquired resistance against many antimicrobials including the last resorts such as carbapenems and colistin. To reduce the progress of resistance rates in E. coli and Klebsiella spp. which are the most common pathogens in community-acquired UTIs, their therapies should be planned according to the results of susceptibility tests as much as possible.Öğe Hospital Outbreak of a Colistin-Resistant, NDM-1-and OXA-48-Producing Klebsiella pneumoniae: High Mortality from Pandrug Resistance(Mary Ann Liebert, Inc, 2018) Guducuoglu, Huseyin; Gursoy, Nafia Canan; Yakupogullari, Yusuf; Parlak, Mehmet; Karasin, Gokhan; Sunnetcioglu, Mahmut; Otlu, BarisColistin resistance causes substantial problems in the treatment of serious infections with carbapenem-resistant (CR) gram-negative bacteria. In this study, we report a fatal hospital outbreak from the spread of a pandrug-resistant Klebsiella pneumoniae clone. An outbreak investigation was conducted after consecutive isolation of nine CR-K. pneumoniae (CR-Kp) strains from eight patients in two intensive care units of a university hospital within 2 weeks. Carbapenem and colistin resistance genes were investigated with PCR, clonal relationships of isolates were studied with pulse-field gel electrophoresis, and multilocus sequence types were determined. The outcomes of the affected patients were analyzed. Genotyping showed a predominant CR-Kp clone consisting of seven strains from six patients. These strains were in ST11 type, an international high-risk clone. They were resistant to all antimicrobials, including colistin, and positive for NDM-1 and OXA-48 carbapenemases, but negative for plasmid-borne colistin resistance genes. One patient had colonization and the remaining five died due to the infection within mean 12 days. No environmental or staff links could be established, and the outbreak was stopped by augmenting infection-control measures. Colistin-resistant K. pneumoniae could clonally expand in the hospital setting, and this spread might be associated with high mortality due to the lack of an appropriate treatment option. Immediate implementation of infection-control measures may be the best way to limit fatal consequences of the spread of such incurable pathogens.Öğe Intravesical hyaluronic acid and chondroitin sulfate alone and in combination for urinary tract infection: Assessment of protective effects in a rat model(Wiley, 2012) Tasdemir, Seda; Tasdemir, Cemal; Vardi, Nigar; Yakupogullari, Yusuf; Duman, Yucel; Parlakpinar, Hakan; Sagir, MustafaObjective: To determine the protective effects of hyaluronic acid and chondroitin sulfate in treating urinary tract infections in a rat model. Methods: A total of 28 rats, which were induced with urinary tract infections through intravesical administration of Escherichia coli, were included in the study. By random selection, they were equally divided into four groups as control (no treatment), hyaluronic acid, chondroitin sulfate and hyaluronic acid + chondroitin sulfate. Bacteriological cultures of the urine and bladder tissue samples were carried out, and the data for each group were statistically compared. Results: In the urine cultures, there were significant differences in median bacterial growth rates in hyaluronic acid (5 x 103 cfu/mL) and chondroitin sulfate (1 x 104 cfu/mL) groups relative to the control group (5 x 104 cfu/mL). However, a significantly lower rate of bacterial colony growth was observed in the hyaluronic acid + chondroitin sulfate group (8 x 102 cfu/mL; P < 0.05). In the bladder tissues, statistically significant decreases in median bacterial growth rates were detected in the hyaluronic acid and hyaluronic acid + chondroitin sulfate groups (both 0 cfu/mg tissue; P < 0.05). Also, transitional epithelium damage decreased in the treatment groups. However, this effect was prominent in hyaluronic acid + chondroitin sulfate group. Conclusion: Our experimental findings show that the hyaluronic acid + chondroitin sulfate combination has a potential benefit in reducing the bacterial load in urine and the thickness of the transitional epithelium.
