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Öğe Antibacterial, antifungal and antimycobacterial activities of some pyrazoline, hydrazone and chalcone derivatives(Walter De Gruyter Gmbh, 2015) Evranos-Aksoz, Begum; Onurdag, Fatma Kaynak; Ozgacar, Selda OzgenTwenty-seven previously reported chalcones and their pyrazoline and hydrazone derivatives as well as two further chalcones have been screened for their antimicrobial, antifungal and antimycobacterial activities against standard microbial strains and drug resistant isolates. The minimum inhibitory concentration (MIC) value of each compound was determined by a two-fold serial microdilution technique. The compounds were found to possess a broad spectrum of antimicrobial activities with MIC values of 8-128 mu g/mL. One compound [(E)-1(4-hydroxyphenyl)-3-p-tolylprop-2-en-1-one] had equal activity with gentamycin (8 mu g/mL) against Enterococcus faecalis. Chalcones were found to be more active than their hydrazone and 2-pyrazoline derivatives against Staphylococcus aureus ATCC 29213 and E. faecalis ATCC 29212.Öğe Antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. isolated from chicken samples(Oxford Univ Press, 2014) Er, Buket; Demirhan, Burak; Onurdag, Fatma Kaynak; Ozgacar, Selda Ozgen; Oktem, Aysel BayhanSalmonella spp. are widespread foodborne pathogens that contaminate egg and poultry meats. Attachment, colonization, as well as biofilm formation capacity of Salmonella spp. on food and contact surfaces of food may cause continuous contamination. Biofilm may play a crucial role in the survival of salmonellae under unfavorable environmental conditions, such as in animal slaughterhouses and processing plants. This could serve as a reservoir compromising food safety and human health. Addition of antimicrobial preservatives extends shelf lives of food products, but even when products are supplemented with adequate amounts of preservatives, it is not always possible to inhibit the microorganisms in a biofilm community. In this study, our aims were i) to determine the minimum inhibitory concentrations (MIC) and minimum biofilm inhibitory concentrations (MBIC) of selected preservatives against planktonic and biofilm forms of Salmonella spp. isolated from chicken samples and Salmonella Typhimurium SL1344 standard strain, ii) to show the differences in the susceptibility patterns of same strains versus the planktonic and biofilm forms to the same preservative agent, and iii) to determine and compare antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. For this purpose, Salmonella Typhimurium SL1344 standard strain and 4 Salmonella spp. strains isolated from chicken samples were used. Investigation of antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. was done according to Clinical and Laboratory Standards Institute M100-S18 guidelines and BioTimer assay, respectively. As preservative agents, pure ciprofloxacin, sodium nitrite, potassium sorbate, sodium benzoate, methyl paraben, and propyl paraben were selected. As a result, it was determined that MBIC values are greater than the MIC values of the preservatives. This result verified the resistance seen in a biofilm community to food preservatives and highlighted this subject, not to be ignored in food applications.Öğe Effect of N-acetylcystein on Antibiofilm Efficiency of Antibiotics in Staphylococci Isolates(Ankara Microbiology Soc, 2021) Kuyucuklu, Gulcan; Onurdag, Fatma Kaynak; Eryildiz, CananBiofilms are often responsible for the difficulties in the treatment of infectious diseases due to their properties that facilitate escape from antibiotic effect and their antiphagocytic effects. At least 65% of all infectious diseases are associated with biofilm-forming bacteria. As Staphylococcus aureus and Staphylococcus epidermidis are among the most common agents of hospital infections and the infections are mostly biofilm-related, they pose an important problem. In infectious isolates, the minimum biofilm eradication concentration (MBEK) values of biofilm forms are much higher than the minimum inhibition concentration (MIC) values of planktonic forms. This situation requires the use of much higher doses of antibiotics in the treatment of infections and causes an increase in antibiotic resistance. The N-acetylcysteine (NAC) molecule is known to be effective against biofilm by disrupting mature biofilms and reducing the adhesion of bacteria to surfaces. In this study, it was aimed to demonstrate i) the biofilm-forming abilities ii) the change in ampicillin and vancomycin MIC values in the presence of NAC molecules, iii) the change in the MBEK values of these antibiotics in the presence of NAC molecule and iv) the change in the expression levels of genes thought to be related to biofilm formation in the presence of the NAC molecule among S.aureus (n= 38) and S.epidermidis (n= 12) isolates isolated from various clinical specimens in Trakya University Health Research and Application Center. In this study, microplate crystal violet method was used to demonstrate the biofilm formation in staphylococci. Broth microdilution and checkerboard method were used to demonstrate the change in the presence of NAC molecule of the MIC and MBEC values of ampicillin and vancomycin. The effect of NAC on the expression of intercellular binding proteins A and D (icaA, icaD) and Staphylococcus regulatory protein A (sarA) genes, which are the genes involved in biofilm formation in staphylococci, was determined by quantitative real-time Polymerase Chain Reaction (qRt-PCR) method. The Student-t test was used to compare the control and experimental groups (concentrations detected with synergy and additive effect); p< 0.05 was accepted as the limit value of significance. In this study, when the NAC molecule was used together with ampicillin and vancomycin, it was determined that this combination lowers the MIC values of staphylococcus isolates and staphylococcal biofilm MBEK values; and also the expression levels of icaA, icaD and sarA which were effective in biofilm formation in staphylococci have not changed and decreased. As a result, in this study, it has been determined that the NAC molecule can be a new alternative for combined drug therapy and is promising in terms of bringing a new approach to treatment. In addition, it is thought that it is possible to use the NAC molecule together with different microorganisms and antimicrobial agents, and the results obtained in this study are considered to be guiding for further studies on this subject.Öğe Effect of Phenylalanine-arginine-beta-naphthylamide to Ciprofloxacin Minimum Inhibitory Concentration Values and Expression of Efflux Pump System Genes in Acinetobacter baumannii Isolates(Ankara Microbiology Soc, 2021) Onurdag, Fatma Kaynak; Kayis, Ugur; Okten, SuzanThe most realistic approach in recent years is researching the resistance inhibition rather than synthesizing new compounds. In this study, we aimed to determine i) the effect of phenylalanine-argininebeta-naphthylamide (PA beta N), on minimum inhibition concentrations (MICs) of ciprofloxacin (CIP), ii) to obtain the CIP+PA beta N concentration that inhibits CIP resistance and iii) to show that this inhibition is caused by the effect of PA beta N on the expression of efflux pump ( EF) system genes. Acinetobacter baumannii isolates were collected from Trakya University Hospital. In 67 isolates determined to be resistant to CIP, CIP susceptibility was investigated in presence of PA beta N once again. Isolates determined to have four or more fold decrease in ciprofloxacin MIC values were included in checkerboard assay and quantitative real-time reverse transcriptase polymerase chain reaction (qrRT-PCR). Fractional inhibition concentrations (FICs) were calculated through the PA beta N concentrations that inhibit ciprofloxacin resistance, by the checkerboard assay results. With the combination of CIP+PA beta N, the effect of the concentrations at which inhibition occurs, to the expression levels of EF system genes (adeA, adeB, adeR, adeS, adeF, adeG, adeH, adeL) was investigated by qrRT-PCR. By the checker board assay, a synergistic effect was determined between PA beta N and CIP in 11 isolates, while in other isolates the effect was determined to be additive. In some isolates resistant to CIP, CIP + PA beta N combination inhibited the resistance and increased CIP susceptibility. In the presence of 25 mg/L and 100 mg/L PA beta N, 22 (32.83%) and 27 (40.3%) of 67 isolates became sensitive to CIP, respectively. In seven isolates, 12.5 mu g/ml PA beta N concentration eliminated CIP resistance by decreasing CIP MIC value to 1 mu g/ml. Also, in one isolate the MIC value was 0.5 mu g/ml in the presence of 25 mu g/ml PA beta N and 1 mu g/ml in the presence of 1.5625 mu g/ml PA beta N. After analyzing the expression levels of EF genes (adeA, adeB, adeC, adeF, adeG, adeH, adeL, adeR and adeS) by the qRt-PCR method, it was determined that with the addition of PA beta N to media containing CIP, the expression levels of the genes decreased (p< 0.05). The aim of the study has been achieved with the results obtained. These results highlighted the importance of research on the inhibition of resistance, as well as the synthesis of new antimicrobial compounds. Combined use of inhibitors and antibiotics should be considered as an alternative treatment method. Thus, existing antibiotics can be included in the treatment again, saving time and money. It will be possible to use these findings in further studies to elucidate the mechanism of action of new inhibitor candidate compounds and associate them with the expression of DAP genes, also by investigating mutations in the regulatory gene regions in isolates with over-expression levels.Öğe Is next generation sequencing an alternative to cultivation-based methods for investigating fungal diversity in indoor air samples?(Springer, 2020) Okten, Suzan; Sen, Burhan; Onurdag, Fatma Kaynak; Kolukirik, Mustafa; Asan, AhmetThe direct effect of fungi on human health makes the fungal diversity in the air an important and necessary subject for examination. Studies that determine fungal diversity generally depends on culture methods. Developed culture-independent methods eliminate many disadvantages of existing culture-dependent methods. In our study, duplicate air samples were collected on 5 different days at a Microbiology Research Laboratory to compare these methods. Samples were collected in 3 different groups: (A) culture method and ITS-targeted Sanger DNA sequencing with 100 L samples, (B) culture method and ITS-targeted Sanger DNA sequencing with 1000 L samples, (C) filter method and next generation sequencing with 1000 L air sample. The Groups A, B and C defines culture, isolation and SANGER DNA-based methods, culture and next generation sequencing methods and directly next generation sequencing methods, respectively. Method-A failed to represent real fungal diversity. Method-B did represent the diversity but did not truly represent relative abundance of the species. Method-C can be completed in 2 days whereas Method-A and B can be completed in 2 weeks and 1 week, respectively. In conclusion, we recommend direct DNA isolation which is followed by ITS-targeted NGS in order to study fungal diversity in indoor air environments.Öğe Salmonella enterica serotypes isolated for the first time in laying hens, and their susceptibility to antibiotics(Elsevier, 2024) Polat, Ibrahim; Sen, Burhan; Onurdag, Fatma KaynakIn this study, a total of 323 drag swab samples were taken from laying hen fresh feces from 3 different provinces (Kirklareli, Edirne, and Tekirdag), which are located in the European part of Tueurorkiye. According to the ISO 6579: 2002 method, 17.3% of the samples were found positive for Salmonella. Obtained 56 Salmonella isolates were serotyped by slide agglutination using antisera according to Kauffmann White Le Minor Scheme. Sixteen sero-types of Salmonella were identified as S. Typhimurium (28.6%), S. Kentucky (17.9%), S. Abony (16.1%), S. Infantis (8.9%), S. Enteritidis (5.4%), S. Anatum (3.6%), S. Saintpaul (3.6%), S. Szentes (1.8%), S. Dibra (1.8%), S. Fallowfield (1.8%), S. Kimuenza (1.8%), S. Escanaba (1.8%), S. Nagoya (1.8%), S. Mbandaka (1.8%), S. Agona (1.8%), and Salmonella II 17: e, n, x, z15: 1,6 (1.8%). Isolations of S. Kimuenza, S. Escanaba, and S. Nagoya from laying hens are reported for the first time in Tueurorkiye. The isolations of S. Dibra, S. Fallowfield, S. Szentes, and Salmonella II 17: e, n, x, z(15): 1,6 from laying hens are the first report in the world. A total of 56 Salmonella isolates were tested for susceptibility to amoxicillin-clavulanic acid, cefepime, azithromycin, cefoxitin, and trimethoprim/sulfamethoxazole by the disk diffusion method. While 10% of S. Kentucky isolates were resistant to ofloxacin, and S. Kimuenza was only resistant to chloramphenicol.Öğe Studies on the synthesis of 3-methyl-6-(substituted-urea/-thiourea)-2(3H)-benzothiazolone derivatives and antimicrobial activities(Natl Inst Science Communication & Information Resources-Niscair, 2015) Unal, Ayse Sibel; Onurdag, Fatma Kaynak; Ozgen, Selda; Dogruer, Deniz; Onkol, TijenA series of sixteen new urea and thiourea derivatives at position 6 of 3-methyl-2(3H)-benzothiazolone ring have been prepared and studied using 1R, H-1 NMR, mass spectra and elemental analysis. The urea and thiourea derivatives have been obtained by the reaction of 6-amino-3-methyl-2(3H)-benzothiazolone with appropriate isocyanates and isothiocyanates. The antibacterial, antifungal and antimycobacterial activities of the synthesized compounds have been evaluated in vitro using microdilution and microplate methods.Öğe Study on Synthesis and Biological Activity of Some Pyridopyridazine Derivatives(Slovensko Kemijsko Drustvo, 2018) Akcay, Sevilay; Ulger, Mahmut; Onurdag, Fatma Kaynak; Dundar, YaseminIn this study, new pyrido [3,4-d]pyridazine derivatives were synthesized and evaluated for their in vitro antibacterial, antifungal and antimycobacterial activities. Among the synthesized compounds, compound 10 (1-(4-benzylpiperazin-1-yl) pyrido [3,4-d]pyridazin-4(3H)-one) and compound 12 (1-(4-benzylpiperidin-1-yl)pyrido [3,4-d]pyridazin-4(3H)-one) were found to have the highest antimycobacterial activity. However, all compounds were found ineffective against tested Gram-positive, Gram-negative bacteria and fungus.Öğe Synthesis and molecular docking studies of some novel antimicrobial benzamides(Academic Press Inc Elsevier Science, 2020) Acar, Cemre; Yalcin, Gozde; Ertan-Bolelli, Tugba; Onurdag, Fatma Kaynak; Okten, Suzan; Sener, Funda; Yildiz, IlkayCommon use of classical antibiotics has caused to the growing emergence of many resistant strains of pathogenic bacteria. Therefore, we aimed to synthesize a number of N-(2-hydroxy-(4 or 5)-nitrophenyl)benzamide derivatives as a new class of antimicrobial compounds. Moreover, our second goal is to predict the interaction between active structures and enzymes (DNA-gyrase and FtsA) in the binding mode. In this study, thirteen N-(2-hydroxy-(4 or 5-nitrophenyl)-substituted-benzamides were synthesized and determined for their antimicrobial activity using the microdilution method. According to this work, none of the compounds showed any activity against Candida albicans and its clinical isolate. Some of the benzamides (4N1, 5N1, 5N2) displayed very significant activity against Staphylococcus aureus and MSSA with < 4 mu g/ml MIC value, even they were found to be more potent than ceftazidime. 4N1 was also found to be more effective than gentamicin against Enterococcus faecalis clinical isolate. Molecular docking studies revealed that 4N1, 5N1, and 5N2 showed a good interactions with DNA-gyrase. Moreover, 5N1 has interacted with FtsA enzyme in the binding mode, as well. Only compound 5N4 displayed very good activity against Escherichia coli ATCC 25922. These findings showed us that 4N1, 5N1, 5N2, and 5N4 could be lead compounds to discover new antibacterial candidates against multidrug-resistant strains.Öğe Synthesis, antimicrobial activity, density functional modelling and molecular docking with COVID-19 main protease studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole(Elsevier, 2021) Zeyrek, Celal Tugrul; Arpaci, Ozlem Temiz; Arisoy, Mustafa; Onurdag, Fatma KaynakThis study contains synthesis, antimicrobial activity, density functional modelling and molecular dock-ing studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. The synthetic procedure of investigated compound is given in detail. The newly synthesized benzoxazole compound and standard drugs were evaluated for their antimicrobial activity against some Gram-positive, Gram-negative bacteria and fungus C. albicans and their drug-resistant isolates. The ben-zoxazole compound has been characterized by using H-1-NMR, IR and MASS spectrometry and elemental analysis techniques. The molecular structure of the compound in the ground state has been modelling using density functional theory (DFT) with B3LYP/6-311 ++ g(d,p) level. The molecular docking of 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole with COVID-19 main protease has been also performed by using optimized geometry and the experimentally determined dimensional struc-ture of the main protease (M-pro) of COVID-19. (C) 2021 Elsevier B.V. All rights reserved.
