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Öğe Characterization of uropathogenic Escherichia coli strains obtained from urology outpatient clinic of Ege Medical Faculty in Izmir(Tubitak Scientific & Technical Research Council Turkey, 2012) Giray, Betul; Ucar, Fusun Bahriye; Aydemir, Sabire SohretAim: To identify the papG gene and its allelic variation in uropathogenic Escherichia coli (UPEC) strains isolated from patients with acute pyelonephritis and cystitis. Materials and methods: Seventy-five E. coli strains isolated from patients admitted to the University of Ege Medical Faculty urology outpatient clinic were isolated and identified phenotypically. All of these strains were examined for the papG gene and allelic distribution of this gene with the multiplex polymerase chain reaction technique. Results: papG genes were found in 24 of 75 E. coli strains. Of these 24 strains, 7 (29%) had papG class II only, 8 (33%) had class III only, and 9 (38%) had both class IT and III. Phylogenetically, it was found that 31 belonged to group B2, 19 to group D, 20 to group A, and 5 to group B1. Serotyping was performed and the positivity was found to be 39%. When the antibiotic resistance profiles of the 75 strains were evaluated, 41 (55%) of them were found to be resistant to ampicillin, 35 (47%) to ciprofloxacin, and 35 (47%) to trimethoprim/sulfamethoxazole. In addition, 23 strains (31%) produced extended-spectrum beta-lactamase. Conclusion: In this study, the rate of papG-positive strains was found to be low. However, there is no consensus on the molecular definition of UPEC. Although the presence of the papG gene indicates that the strains are UPEC, absence of the papG gene does not suggest that the strains are not UPEC.Öğe Determination and comparison of microbial loads in atmospheres of two hospitals in Izmir, Turkey(Inst Agricultural Medicine, 2013) Cakir, Nerguze Aydin; Ucar, Fusun Bahriye; Uztan, Alev Haliki; Corbaci, Cengiz; Akpinar, OnurIntroduction and Objectives. Nosocomial infections, also known as hospital-acquired infections, has become one of the most important health problems in health care units worldwide. The presented study aims to determine the average amount of microorganism loads and to show that the atmospheres of the two hospitals can be a potential source regarding nosocomial infections. The effect of surface and floor disinfection processes in the two hospitals and the antibiotic susceptibility of the bacterial isolates were also evaluated. Materials and Methods. Microorganisms were isolated from air samples collected from different areas (patient wards, corridors, operating theatres and postoperative units) of the two hospitals in Izmir. Sampling was conducted between December 2006 March 2007. Results. During the 3-month sampling period, the average number of live microorganisms in the air samples collected from second-class environments in the hospital 1 and the hospital 2 was found to be 224.44 and 536.66 cfu/m(3), respectively. The average number of microorganisms in hospital 2 collected before the disinfection process was higher than those after the disinfection process. However, because of the closure of the air-conditioning system and the hepa filters after the disinfection process, this was reversed in hospital 1. In total, 54 and 42 isolates were obtained from hospital 1 and hospital 2, respectively. 49 isolates from hospital 1 and 35 isolates from hospital 2 were identified as Staphylococcus sp. The remaining isolates were identified as Aerococcus sp. and Entero coccus sp. Pseudomonas sp. was not determined in the air samples of the two hospitals. Conclusions. It was detected that the microbial loads in the atmospheres of the two hospitals studied varied greatly depending on the number of people in the environment. As the results indicate, the total number of microorganisms in the atmospheres of operating theatres in both hospitals does not pose a threat according to the Air Microbe Index.Öğe Determination and comparison of microbial loads in atmospheres of two hospitals in Izmir, Turkey(Inst Agricultural Medicine, 2013) Cakir, Nerguze Aydin; Ucar, Fusun Bahriye; Uztan, Alev Haliki; Corbaci, Cengiz; Akpinar, OnurIntroduction and Objectives. Nosocomial infections, also known as hospital-acquired infections, has become one of the most important health problems in health care units worldwide. The presented study aims to determine the average amount of microorganism loads and to show that the atmospheres of the two hospitals can be a potential source regarding nosocomial infections. The effect of surface and floor disinfection processes in the two hospitals and the antibiotic susceptibility of the bacterial isolates were also evaluated. Materials and Methods. Microorganisms were isolated from air samples collected from different areas (patient wards, corridors, operating theatres and postoperative units) of the two hospitals in Izmir. Sampling was conducted between December 2006 March 2007. Results. During the 3-month sampling period, the average number of live microorganisms in the air samples collected from second-class environments in the hospital 1 and the hospital 2 was found to be 224.44 and 536.66 cfu/m(3), respectively. The average number of microorganisms in hospital 2 collected before the disinfection process was higher than those after the disinfection process. However, because of the closure of the air-conditioning system and the hepa filters after the disinfection process, this was reversed in hospital 1. In total, 54 and 42 isolates were obtained from hospital 1 and hospital 2, respectively. 49 isolates from hospital 1 and 35 isolates from hospital 2 were identified as Staphylococcus sp. The remaining isolates were identified as Aerococcus sp. and Entero coccus sp. Pseudomonas sp. was not determined in the air samples of the two hospitals. Conclusions. It was detected that the microbial loads in the atmospheres of the two hospitals studied varied greatly depending on the number of people in the environment. As the results indicate, the total number of microorganisms in the atmospheres of operating theatres in both hospitals does not pose a threat according to the Air Microbe Index.Öğe Genotypic analysis of Escherichia coli strains that cause urosepsis in the Aegean region(Tubitak Scientific & Technical Research Council Turkey, 2016) Giray, Betul; Ucar, Fusun Bahriye; Aydemir, Sabire SohretBackground/aim: The aim of this study was to characterize strains genotypically, to determine their phylogenetic relationships, to investigate the presence of the papG gene, and to compare their antibiotic susceptibility test results. Materials and methods: Seventy pathogenic E. coli strains were isolated from both urine and blood cultures of patients with the preliminary diagnosis of urosepsis who were referred to the Ege University Faculty of Medicine, Bacteriology Laboratory of Medical Microbiology Department in Izmir. All of these strains were examined for the papG gene and phylogenetic groups with the multiplex polymerase chain reaction technique. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used for epidemiologic analysis. Results: Phylogenetically, it was found that 16 belonged to group B2, 31 belonged to group D, 15 belonged to group A, and 7 belonged to group B1. One strain was not identified as belonging to a group. papG genes were found in 26 of 70 E. coli strains. Thirty urosepsis pathogenic E. coli strains were analyzed with MLST. Twenty-two strains were identified as new STs. Conclusion: These findings are extremely important for Turkey and these new 22 strains should be investigated in more detail because they are new and have the potential to lead to infections.Öğe Molecular characterization of Yarrowia lipolytica strains isolated from different environments and lipase profiling(Tubitak Scientific & Technical Research Council Turkey, 2013) Akpinar, Onur; Ucar, Fusun BahriyeIn order to analyze yeasts that produce industrial compounds, it is essential to identify them accurately. Yarrowia lipolytica is one of the most extensively studied "nonconventional" yeasts, being a strictly aerobic microorganism capable of producing important metabolites and having an intense secretory activity, which justifies efforts to use it in industry (as a biocatalyst), in molecular biology, and in studies of genetics. Therefore, in this study, an accurate identification of Y. lipolytica strains was performed using 3 different molecular biological methods (RFLP analysis of ITS1-5.8S rDNA-ITS2 and 18S rDNA regions and sequencing of the D1/D2 domain of the 26S rDNA region). The 26S rRNA gene sequence of the strains showed sequence homology with various Y. lipolytica strains from the National Center for Biotechnology Information. A number of different lipids (tributyrin, olive oil, and fish oil) were screened in terms of the growth of Y. lipolytica strains and lipase production. It was determined that all lipid-related substrates supported lipase production levels ranging from 4.27 U/mL (tributyrin) to 37.08 U/mL (fish oil). Fish oil (1%) showed maximum specific activity in the supernatant (264.85 U/mg of protein) and TEM TAN 46. The Y. lipolytica strain that was produced in the media containing fish oil was found to be the best lipase producer.Öğe Molecular characterization of Yarrowia lipolytica strains isolated from different environments and lipase profiling(Tubitak Scientific & Technical Research Council Turkey, 2013) Akpinar, Onur; Ucar, Fusun BahriyeIn order to analyze yeasts that produce industrial compounds, it is essential to identify them accurately. Yarrowia lipolytica is one of the most extensively studied "nonconventional" yeasts, being a strictly aerobic microorganism capable of producing important metabolites and having an intense secretory activity, which justifies efforts to use it in industry (as a biocatalyst), in molecular biology, and in studies of genetics. Therefore, in this study, an accurate identification of Y. lipolytica strains was performed using 3 different molecular biological methods (RFLP analysis of ITS1-5.8S rDNA-ITS2 and 18S rDNA regions and sequencing of the D1/D2 domain of the 26S rDNA region). The 26S rRNA gene sequence of the strains showed sequence homology with various Y. lipolytica strains from the National Center for Biotechnology Information. A number of different lipids (tributyrin, olive oil, and fish oil) were screened in terms of the growth of Y. lipolytica strains and lipase production. It was determined that all lipid-related substrates supported lipase production levels ranging from 4.27 U/mL (tributyrin) to 37.08 U/mL (fish oil). Fish oil (1%) showed maximum specific activity in the supernatant (264.85 U/mg of protein) and TEM TAN 46. The Y. lipolytica strain that was produced in the media containing fish oil was found to be the best lipase producer.Öğe Production of citric and isocitric acid by Yarrowia lipolytica strains grown on different carbon sources(Walter De Gruyter Gmbh, 2014) Celik, Gonul; Ucar, Fusun Bahriye; Akpinar, Onur; Corbaci, CengizObjective: The goal of this study was to determine the influence of various carbon sources on the citric and isocitric acid production by various Yarrowia lipolytica strains. Methods: The yeasts used in our study were first investigated for organic acid production using screening media. Then, the effect of several complex carbon sources on the citric and isocitric acid production of selected yeast strains was investigated. The amount of citric and isocitric acid production was determined via enzymatic reactions. Results: In this study, 22 Y. lipolytica strains were investigated for the organic acid production. Among these strains, 2 strains (TEM YL 3 and TEM YL 20) were found to be highest organic-acid producer. Taken all results together, the highest amounts of citric acid (66.2 g/L for TEM YL 3, 50.0 g/L for TEM YL 20) were observed in the production medium containing sunflower oil. Conclusion: Citric acid consumption, and thus, the need for it are constantly rising in our country, which imports citric acid. Therefore, in order to meet this need, further studies which will yield to the maximum citric acid production should be performed by utilizing waste carbon sources and by using new low- cost but high citric acid-producing strains.Öğe Screening and molecular characterization of polycyclic aromatic hydrocarbons degrading yeasts(Walter De Gruyter Gmbh, 2015) Boz, Digdem Tunali; Yalcin, Husniye Tansel; Corbaci, Cengiz; Ucar, Fusun BahriyeObjective: Disasters such as leakages and accidental falls are the main causes of environmental pollution by the petroleum industry product. Since no commercial yeast strain with biodegradation capacity is available, we aimed to isolate and characterize hydrocarbon degrading yeasts. Methods: Yeast isolates used in the study were isolated from samples of wastewater, active sludge and crude oil, which was obtained from a petroleum refinery as well as from soil samples, which were contaminated with crude oil. Yeast isolates used in the study were isolated from wastewater, active sludge and petroleum samples obtained from petroleum refinery and soil samples contaminated with petroleum. Degradation of naphthalene, phenanthrene, pyrene and crude petroleum by yeasts were determined using a microtiter plate-based method. Molecular characterization was achieved by performing a sequence analysis of the ITS1-5.8S rRNA-ITS2 and 26S rRNA regions. Results: In total, 100 yeast isolates were obtained from four different samples. Following the incubation in media containing different polycyclic aromatic hydrocarbon compounds (naphthalene, phenanthrene, pyrene) and crude petroleum, 12 yeast isolates were detected to degrade more than one polyaromatic hydrocarbon. Sequence analyses of rRNA regions revealed that the identified yeasts represented 10 species belonging to 6 genera. The isolates were identified as Candida parasilopsis, Candida sinolaborantium, Cryptococcus albidus, Cryptococcus diffluens, Cryptococcus uzbekistanensis, Pichia kudriavzevii, Rhodosporidium diobovatum, Rhodotorula glutinis, Rhodotorula muciloginosa and Saccharomyces cerevisiae. Conclusion: Yeast strains that are capable of degrading more than one polycyclic aromatic hydrocarbon compound have the potential of being utilized in future research.Öğe Star network analysis of sequence based identified Yarrowia lipolytica strains(Walter De Gruyter Gmbh, 2014) Akpinar, Onur; Haliki, Emir; Ucar, Fusun Bahriye; Uztan, Alev HalikiAim: The objectives of this study are, first, to investigate a star network analysis of phylogenetic trees of identified Y. lipolytica strains with or without one out-group, and secondly, to show the redundancy of the out-groups in phylogenetic tree. Material and Methods: In this study we used 22 Yarrowia lipolytica strains which were identified with sequencing of D1/D2 domain of 26S rDNA region, two phylogenetic trees were reconstructed by the neighbor joining method including an out-group or not. The starlike weighted network analysis of these two phylogenetic trees was investigated. Results: The adjacency matrix formalism of our weighted phylogenetic network with the out-group looks like a directed star graph adjacency matrix. The lowest weight is the edge from the central node to Candida sake out-group (0.00008) corresponding to the narrowest edge. However, the edge going from central node to Yarrowia lipolytica TEM YL 19 has a weight of 0.0825 and the thickest structure. Conclusion: Thus network analysis show that phylogenetic relationship between close strain and subspecies can be confirmed and also the out-group in this phylogenetic tree is unnecessary due to the negligible change in the average weighted degree and its some statistical computations.
