Sürdürülebilir Kalkınma Amaçları
Yayınlar
- MakaleAçık Erişim2026Whole-genome characterization of clinical Enterococcus faecalis and Staphylococcus epidermidis Isolates reveals mecA-positive E. faecalis and a shared lnu(A)–rep7a resistance plasmid in Türkiye
Ejder, Nebahat; Özad Düzgün, Azer
Background: This study aimed to genomically characterize clinical Enterococcus faecalis and Staphylococcus epidermidis isolates obtained from aspirate and sputum samples at Bayburt State Hospital, focusing on antimicrobial resistance genes, virulence factors, and mobile genetic elements. Methods: Whole-genome sequencing (WGS) was performed on the isolates, and antimicrobial resistance genes, virulence determinants, multilocus sequence types (MLST), plasmid replicons, and mobile genetic elements were identified using bioinformatics tools. Results: The E. faecalis E5 (ST64) isolate, recovered from an aspirate sample, carried multiple antimicrobial resistance genes, including mecA, vanT, erm(B), tet(M), and qacA, along with a diverse virulence gene repertoire (cyl, ebp, ace, and agg), mobile genetic elements (Tn6009, ISL1a3), and four plasmid replicons (rep19C, rep9C, repUS43, and rep7a). The E. faecalis E184 and E187 isolates (ST124), obtained from sputum samples, harbored fewer acquired resistance genes but shared gyrA (T672A) and parC (V307I) mutations associated with fluoroquinolone resistance. The S. epidermidis ST59 isolate carried resistance genes lnu(A), fosB, and qacD, together with the plasmid replicon rep7a and insertion sequence ISSau4. The co-occurrence of lnu(A) and the rep7a plasmid in both species suggests a potential pathway for interspecies transmission of resistance determinants. Conclusions: This study reports the genomic detection of mecA in an E. faecalis isolate from Türkiye based on WGS analysis. However, this finding is based solely on genomic data and lacks phenotypic or experimental validation. The detection of a shared plasmid-associated resistance element (lnu(A)–rep7a) in both E. faecalis and S. epidermidis highlights the potential for interspecies resistance gene flow within the hospital environment.
- MakaleAçık Erişim2025Investigation of virulence factor genes and biofilm formation of antibiotic resistant clinical E.coli isolates
Mumin, Yahye Mohamud; Yüksel, Gamze; Özad Düzgün, Azer
Purpose: The aim of this study is to investigate the antibiotic sensitivity, presence of virulence genes and biofilm formation capacity of 90 clinical E. coli isolates. Methods: The presence of virulence genes in E. coli isolates were investigated by PCR. Ninety clinical isolates of E. coli were subjected to biofilm quantitative analysis using the semi-quantitative crystal violet staining method. Results: it was observed that the isolates were resistant to quinolone, cephalosporin, aminoglycoside, carbapenem and penicillin group antibiotics. The presence of virulence factor genes were observed in a total of 86/90 E. coli. The highest rate of fim (92.2 %) virulence factor gene was detected in the strains. Afa, pap, cnf, sfa, hly were detected in 30 %, 13 %, 13 %, 3.3 %, 2.2 % respectively. Also, 13 different virulence factor gene patterns were determined in 90 E. coli isolates. Of the 90 E. coli isolates whose biofilm-forming capacities were evaluated, 42 were found to have biofilm-forming capacity. Of these 26 (28.8 %) the weak, 12 (13.3 %) moderate and 4 (4.4 %) strong biofilm-forming. Also, statistical analysis was performed to investigate the relationship between virulence factor genes and biofilm formation, and none of the 7 genes analyzed showed a significant relationship with biofilm formation. Conclusion: since pathogenic E. coli is an important public health problem, investigating antibiotic resistance, virulence factor genes and biofilm formation in bacterial pathogens is important for better treatment options.
- MakaleAçık Erişim2024Investigation of Antibiofilm and Antibacterial Properties of Green Synthesized Silver Nanoparticles from Aqueous Extract of Rumex sp.
Akay, Seref; Yüksel, Gamze; Özad Düzgün, Azer
The decrease in the effectiveness of conventional drugs as a result of the growth of resistance to antibiotics has increased the need for innovative tools to control the infections. At this point, metallic nanoparticles, in particular silver nanoparticles, have appeared as a promising method. In the current study, the extract of Rumex sp. (Labada, dock) leaves was used as a reducing agent for the formation of silver nanoparticles. Unlike similar studies, in this study the synthesis conditions were optimized by changing the extract ratio and silver nitrate concentration. Morphological investigations of synthesized silver nanoparticles showed that spherical homogeneous particles at size under 100 nm had been produced. SEM/EDS and FTIR analyses showed that plant components are involved in the synthesis of nanoparticles. It was also determined that higher extract ratio reduced nanoparticle size. The antimicrobial effects of the synthesized nanoparticles against Gram-positive and Gram-negative bacteria were tested, and it was determined that all nanoparticles exhibited activity against both groups. Rumex sp. silver nanoparticles (NPs) were revealed to exhibit antibiofilm activity against three different isolates with moderate and strong biofilm-forming ability. The NPs reduced the biofilm-forming capacity of Acinetobacter baumannii and Klebsiella pneumonaie by 2.66-fold and 3.25-fold, whereas they decreased the Escherichia coli biofilm-forming capacity by 1.25-fold. The investigation of microbial biofilm could play an important role in developing new strategies for treatment options. Our results suggest that Rumex sp. silver NPs may have a high potential for use in the treatment of pathogenic strains.
- MakaleAçık Erişim2024Determination of the Cytotoxicity and Antibiofilm Potential Effect of Equisetum arvense Silver Nanoparticles
Akar, Zeynep; Akay, Seref; Ejder, Nebahat; Özad Düzgün, Azer
This study aimed to synthesize and characterize silver nanoparticles (AgNPs) by green synthesis from Equisetum arvense (Ea) extracts and to investigate their cytotoxicity, antibiofilm activity, and α-glucosidase enzyme inhibition. Diverse characterization techniques were applied to verify the production of nanoparticles. SEM examination confirmed that the size of nanoparticles is in the range of 40–60 nm. Also, interactions between silver and natural compounds of plant extract were confirmed through FT-IR and EDX analyses. It was determined that Equisetum arvense silver nanoparticles had antibiofilm activity against three different clinical strains with high biofilm-forming ability. AgNPs reduced the biofilm-forming capacity of clinical A. baumannii isolate with strong biofilm-forming capacity by approximately twofold, while the capacity of clinical K.pneumonaie and E.coli isolates decreased by 1.5 and 1.2 fold, respectively. The α-glucosidase enzyme inhibition potential of the AgNPs, which is determined as 93.50%, was higher than the plant extract with, and the α- 30.37%. MTT was performed to assess whether incubation of nanoparticles with A549 and ARPE-19 cell lines affected their viability, and a dramatic reduction in cell growth inhibition of both A549 and ARPE-19 cells was observed. It has been shown that A549 cells treated with 200 and 150 µg/mL nanoparticles had less cell proliferation compared to control cells at 24-h and 48-h incubation time. According to these results, Ea-derived AgNPs appear to have potential anticancer activity against A549 cancer cells. Investigating the effects of green synthesis nanoparticles on microbial biofilm and various tumors may be important for developing new therapies. The outcomes of this study have showed that Ea-AgNPsmay have a high potential both in the treatment of pathogenic strains that form biofilms, as well as in anticancer therapy use.
- MakaleAçık Erişim2023Detection of virulence factor genes, antibiotic resistance genes and biofilm formation in clinical Gram-negative bacteria and first report from Türkiye of K.oxytoca carrying both bla OXA-23 and bla OXA-51 genes
Özad Düzgün, Azer; Yüksel, Gamze
The Gram-negative bacteria were isolated from various samples and antibiotic susceptibility testing were performed. The strains were screened by PCR for class 1 integron, virulence and antibiotic resistance genes. blaOXA-23 and blaOXA-51 genes positive samples were cloned into the pGEM-T vector and the plasmids were sent for DNA sequence analysis. The isolates were showed resistance to quinolone, cephalosporin, aminoglycoside, carbapenem and penicillin group antibiotics. Virulence factor genes were identified in 121 strain. The most common virulence gene was determined to be aer (29.78%), followed by sfa (28.19%), afa (27.12%), cnf (21.27%), pap (12.76%) and hly (12.76%). In addition, 34 different virulence patterns were observed. Plasmid-mediated quinolone resistance genes were detected 15 of67 quinolone-resistant isolates. Among carbapenem resistant strains, blaOXA-23 gene was detected in 16 and blaOXA-51 gene in 19 isolates. The strains producing OXA-23 and OXA-51 were Klebsiella oxytoca, Acinetobacter baumannii, E.coli and P.mirabilis. In this study, clinical isolate K. oxytoca carrying both blaOXA-23 and blaOXA-51 genes were identified first time from Türkiye. A high predominance (88.82%) of class 1 integron was detected. In addition, determined that 46.27% of the isolates had the ability to form biofilms. In conclusion since the limited treatment options of antibiotic-resistant Gram-negative pathogens that cause serious infections are an important problem in terms of public health it is important to investigate antibiotic resistance, virulence factor genes and biofilm formation in these pathogens.
- MakaleAçık Erişim2023First report of qnr and blaVIM-4-like producing clinical Alcaligenes faecalis isolated in Türkiye; [Türkiye'den izole edilen qnr ve blaVIM-4-like üreten klinik Alcaligenes faecalis’in ilk raporu]
Akyildiz, Esma; Saral Sariyer, Ayşegül; Köse, Tuba; Arslan, Mikail; Beriş, Fatih Şaban; Özad Düzgün, Azer
The study set out to look at the clinical strain of A. faecalis's antibiotic susceptibility pattern. Both biochemical and molecular approaches were used to identify A.faecalis. The VITEK compact system was used to analyze the strain's antibiotic susceptibility profile. The use of PCR was evaluated to determine the presence of resistance genes. It was also determined whether resistance determinants could be transferred. It was determined that A. feacalis showed resistance to imipenem, cefepime, ceftazidime, gentamicin, amikacin, netilmicin, tobramicin, ciprofloxacin, and levofloxacin. The blaVIM-4-like gene was present in this strain, according to the results of the PCR and DNA sequencing studies. In contrast to VIM-4, this blaVIM-4-like gene showed one amino acid change (Ala265Val).Filter-mating experiments showed that the blaVIM-4-like gene cannot be transferred from A. faecalis to E. coli. In this study, This research, demonstrated the presence of the blaVIM-4-like gene for the first time in A. faecalis from Turkey.
- MakaleYalnız künye2022In vitro and in silico evaluation of some plant extracts and phytocompounds against multidrug-resistant Gram-negative bacteria
Aydemir, Eda; Sarıyer, Emrah; Akyıldız, Esma; Özad Düzgün, Azer; Camadan, Yasemin; Saral Sarıyer, Ayşegül
The spread of multidrug-resistant Gram-negative (MDR) bacteria is a global public health problem, as infections caused by MDR Gram-negative bacteria are difficult to treat. New antibiotic agents need to be developed to overcome this problem, and phytochemicals show promise at this point. In this study, methanol extracts were prepared from cinnamon, thyme, nettle, white tea, rosehip, and antibacterial activity of the methanol extracts was studied against two MDR Gram-Negative bacteria (K. pneumoniae and A. baumannii) by broth microdilution method. The MICs of methanol extracts of cinnamon, rosehip, thyme, white tea for A. baumannii were found as 0.015125 g/ml, 0.07825 g/ml, 0.030625 g/ml, 0.00796875 g/ml, respectively. It was found that only cinnamon methanol extract had antibacterial activity in the used extract concentrations against K. pneumoniae and the MIC value was 0.0605 g/ml. The effects of plant methanol extract with antibacterial activity and imipenem combinations were studied in vitro using the checkerboard method. The FIC Indexes were obtained from the checkerboard results and it was observed that the combination of methanol extract and imipenem showed an antagonistic or additive/indifferent effect but not a synergistic effect. We evaluated the binding affinity of epigallocatechin 3-gallate, quercetin, cinnamaldehyde, carvacrol, and thymol phytocompounds using in silico methods, which are well known as a phytocompounds in white tea, cinnamon, thyme, nettle, and rosehip and have antibacterial activities. The results suggested that these phytocompounds should be supported with in vivo and in vitro experiments to investigate their potential for being inhibitor candidates.
- MakaleYalnız künye2021From Turkey: First Report of KPC-3-and CTX-M-27-Producing Multidrug-Resistant Klebsiella pneumoniae ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations
Özad Düzgün, Azer
Aim: The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant Klebsiella pneumoniae strain. Materials and Methods: Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Multilocus sequence typing analysis was carried out using seven conserved housekeeping genes. Results: The strain was resistant to penicillins, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and trimethoprim/sulfamethoxazole. The isolate was found to carry KPC-3, CTX-M-27, SHV-11, SHV-67, and TEM-1 β-lactamases. The clonal subtype of the isolate was ST147, and it possessed wzi64 and wzc38 alleles. Fifteen different point mutations (N49S, L59V, R146H, V178P, G189T, F198Y, V202L, F207Y, A217S, T222L, D223G, H235N, A280V, N304E, and S346N) were detected in the OmpK36 porin. A frame shift was observed in OmpK35 and two different point mutations (I70M and I128M) were found in the OmpK37 porin, in addition to seven mutations observed on the AcrR. Conclusions: This study demonstrated for the first time that the ST147 clone produced CTX-M-27 as well as KPC-3. In addition, new mutations were detected in the outer membrane proteins. These mutations together with the production of extended-spectrum β-lactamase and carbapenemase were found to contribute to the resistance of the ST147 clone to carbapenem and other antibiotics.
- MakaleAçık Erişim2019Determination of antibiotic resistance genes and virulence factors in Escherichia coli isolated from Turkish patients with urinary tract infection
Özad Düzgün, Azer; Okumuş, Funda; Saral, Ayşegül; Çopur Çiçek, Ayşegül; Cinemre, Sedanur
Introduction: Escherichia coli ranks among the most common sources of urinary tract infections (UTI). Methods: Between November 2015 and August 2016, 90 isolates of E. coli were isolated from patients at Rize Education and Research Hospital in Turkey. Antibiotic susceptibility was determined for all isolates using the Kirby-Bauer disk diffusion method. These E. coli isolates were also screened for virulence genes, β-lactamase coding genes, quinolone resistance genes, and class 1 integrons by PCR. Results: With respect to the antibiotic resistance profile, imipenem and meropenem were effective against 98% and 90% of isolates, respectively. A high percentage of the isolates showed resistance against β lactam/β lactamase inhibitor combinations, quinolones, and cephalosporins. PCR results revealed that 63% (57/90) of the strains carried class 1 integrons. In addition, a high predominance of extended-spectrum β-lactamases (ESBLs) was observed. The qnrA, qnrB, and qnrS genes were found in 24 (26.6%), 6 (6.6%), and 3 (3.3%), isolates, respectively. The most common virulence gene was fim (82.2%).The afa, hly, and cnf1 genes were detected in 16.6%, 16.6%, and 3.3% of isolates, respectively. Moreover, we observed eleven different virulence patterns in the 90 E. coli isolates. The most prevalent pattern was fim, while hly-fim, afa-aer-cnf-fim, aer-cnf, afa-aer, and afacnf- fim patterns were less common. Conclusions: Most of the E. coli virulence genes investigated in this study were observed in E. coli isolates from UTI patients. Virulence genes are very important for the establishment and maintenance of infection.