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    A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination
    (Springer, 2023) Büyük, Fatih; Karakaya, Emre; Akar, Mustafa; Kayman, Tuba; Tarhane, Serdal; Özcan, Hacer Ece; Çelebi, Özgür
    Helicobacter pylori is a pathogen associated with gastroduodenal diseases. This study aimed; (i) to investigate H. pylori presence by invasive tests in adult dyspeptic patients, (ii) to determine antibiotic susceptibility and genotypic characteristics of the H. pylori isolates, and (iii) to investigate the relationship between the H. pylori genotypes and the histopathological findings. In this cross-sectional study, gastric biopsy samples from 208 adult dyspeptic patients were used for culture, tissue Polymerase Chain Reaction (PCR), and histopathological analysis. Antibiotic susceptibility of the H. pylori isolates was analyzed by gradient method. Analysis of the virulence genes was performed by monoplex PCR. Genetic profiles (from A to H) were created based on the virulence genes presence. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) was used for the genotyping of the H. pylori isolates. The mean age of the patients was 46 (& PLUSMN; 15) years and 128 (61.5%) of them were female. H. pylori positivity was detected by culture, tissue PCR and histopathological examination in 59 (28.4%), 114 (54.8%) and 81 (38.9%) patients, respectively. The overall prevalence of H. pylori was found to be 63% (131/208). All H. pylori isolates were susceptible to tetracycline and amoxicillin. The resistance rates for metronidazole, clarithromycin, levofloxacin, and rifampicin were 67.2%, 27.9%, 34.4% and 13.11%, respectively. Multi drug resistance (MDR) was detected at the rate of 45.9% (28/61). While the most common virulence gene was cagA (93.44%), the least common was vacAm1 (23%). The predominant genetic profile was profile A (47.5%). ERIC-PCR results revealed a total of 26 different patterns. A high prevalence of H. pylori was detected in adult dyspeptic patients as in developing countries. It was observed significant genotypic heterogeneity and virulence gene diversity within the isolates. A considerable resistance rate detected against antibiotics such as clarithromycin, metronidazole, and levofloxacin, which are frequently used in the eradication of H. pylori, should be taken into consideration when creating regional empirical treatment regimens.
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    A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination (vol 116, pg 1261, 2023)
    (Springer, 2023) Büyük, Fatih; Karakaya, Emre; Akar, Mustafa; Kayman, Tuba; Tarhane, Serdal; Özcan, Hacer Ece; Çelebi, Özgür
    [Abstract No tAvailable]
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    Correction: A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination (Antonie van Leeuwenhoek, (2023), 116, 12, (1261-1273), 10.1007/s10482-023-01868-3)
    (Springer Science and Business Media Deutschland GmbH, 2023) Buyuk, Fatih; Karakaya, Emre; Akar, Mustafa; Kayman, Tuba; Tarhane, Serdal; Ozcan, Hacer Ece; Celebi, Ozgur
    In the original publication of the article, the Fig. 1 text citation was incorrectly provided in the section “Virulence genes analysis”. However, it should have been Fig. 2. The Fig. 2 text citation was incorrectly provided in the section “Clinical data and diagnostic tests results”. However, it should have been Fig. 1. In the section “Antimicrobial testing results”, Fig. 2 text citation is removed. The figures 1 and 2 have been swapped correctly. The original article has been corrected. © 2023, Springer Nature Switzerland AG.
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    Escherichia coli in different animal feces: phylotypes and virulence genes
    (Springer, 2023) Karakaya, Emre; Aydin, Fuat; Kayman, Tuba; Abay, Secil
    In this study, it was aimed to determine the phylogroups of Escherichia coli isolates from horse, cat, dog, sheep, cattle, and chicken feces samples and to investigate some important virulence genes of the isolates. For this purpose, a total of 600 feces samples, 100 from each animal species, were used as material. For the isolation of E.coli, feces samples were directly inoculated on MacConkey agar. The identification of the isolates was performed via phenotypic tests and species-specific multiplex Polymerase Chain Reaction (mPCR) method. PCR methods were used to phylotype E.coli isolates and to investigate virulence genes (bfpA, eaeA, LT, ST, Stx1, and Stx2). Of the total 600 E.coli isolates recovered in this study, 120 (20%), 269 (44.8%), 58 (9.7%), 19 (3.2%), 35 (5.8%), 56 (9.3%), 31 (5.2%), and 12 (2%) were identified as phylogroup A, B1, B2, C, D, E, F, and Escherichia clade I, respectively. While the virulence gene was detected in 149 (24.8%) E.coli isolates, no virulence gene was detected in 451 (75.2%) isolates. According to the analysis results, the most determined virulence gene was Stx1, while the least determined virulence gene was LT. In conclusion, in this study, when both the animal species and the number of E.coli isolates examined are considered, the data obtained are of great importance in epidemiological terms. However, the detection of virulence genes in 13.5% among phylogroup A, B1, and C isolates with commensal characteristics suggest that these isolates may show pathogenic characteristics with the virulence genes they contain.
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    Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species
    (Elsevier Gmbh, 2024) Aydin, Fuat; Tarhane, Serdal; Karakaya, Emre; Abay, Secil; Kayman, Tuba; Guran, Ozgur; Bozkurt, Emin
    It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in T & uuml;rkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6T, which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75T and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75T and their close neighbors H.anseris ATCC BAA-1299T shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75T in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75T (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature.
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    MLST genotypes and quinolone resistance profiles of Campylobacter jejuni isolates from various sources in Turkey
    (Elsevier, 2023) Aydin, Fuat; Kayman, Tuba; Abay, Secil; Hizlisoy, Harun; Saticioglu, Izzet Burcin; Karakaya, Emre; Sahin, Orhan
    This study was conducted to determine the overall genetic diversity, as well as prevalence and mechanisms of resistance to quinolone antibiotics of 178 Campylobacter jejuni isolated from humans, cattle, dogs, and chickens in Turkey. Multilocus sequence typing (MLST) and E-test were performed for genotyping and antimicrobial susceptibility testing, respectively. Mismatch Amplification Mutation Assay, Polymerase Chain Reaction (MAMAPCR) was used to detect point mutations associated with quinolone resistance. Of the 178 isolates tested, 151 were included in 21 clonal complexes (CCs); the remaining 27 isolates did not belong to any existing CCs. CC21, CC353, CC206, and CC257 were the predominant clones, representing 38 % of all C. jejuni isolates tested. The isolates were assigned to 78 different sequence types (STs), three of which were novel (ST 8082, ST 8083, and ST 8084). Resistance to quinolones was found in 73 (41 %) of the isolates (42.85 %, 2.85 %, 20.58 %, and 43.75 % in human, cattle, dog, and chicken isolates, respectively). All of the resistant isolates had Thr-86-Ile mutation in the gyrA gene. The highest Sorensen coefficient index was detected for human/chicken meat and human/dog C. jejuni isolates (Ss = 0.71), suggesting a strong link between the isolates from respective sources. The Simpson diversity index of C. jejuni isolates analyzed was detected between 0.92 and 0.98.The study provides detailed information on the quinolone resistance and MLST-based genetic relatedness of C. jejuni isolates from humans, cattle, dog, and broiler meat in Turkey for the first time, enabling a better understanding of the transmission pathways of C. jejuni in this country. Our results suggest that broiler meat and dogs may be the most important sources of human campylobacteriosis in Turkey.
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    The canonical Brucella species-host dependency is changing, however, the antibiotic susceptibility profiles remain unchanged
    (Academic Press Ltd- Elsevier Science Ltd, 2023) Celik, Elif; Kayman, Tuba; Buyuk, Fatih; Saglam, Aliye Gulmez; Abay, Secil; Akar, Mustafa; Karakaya, Emre
    Brucellosis is a chronic disease caused by Brucella species with a wide range of hosts, from marine mammals to terrestrial species, but with strict host preferences. With the zoonotic character, the prevalence of human brucellosis cases is a reflection of animal infections. This study aimed to identify 192 Brucella isolates obtained from various sources by Bruce-ladder PCR and to determine their antibiotic susceptibilities by gradient diffusion method (E-test). As a result of the PCR, all human isolates (n = 57) were identified as B. melitensis. While 58 (82.9%) of the cattle isolates were identified as B. abortus, 59 (90.8%) of the sheep isolates were identified as B. melitensis. In addition, 12 (17.1%) of the cattle isolates and 6 (9.2%) of the sheep isolates were determined as B. melitensis and B. abortus, respectively. The primary host change behavior of B. melitensis was 1.9 times higher than that of B. abortus. While gentamicin and ciprofloxacin susceptibilities of Brucella isolates were 100%, tetracycline, doxycycline, streptomycin, trimethoprim/sulfamethoxazole and rifampicin susceptibilities were 99%, 99%, 97.4%, 91.7% and 83.9%, respectively. The lowest sensitivity of the isolates was determined against to cefoperazone as 26%. A triple-drug resistance was detected in 1 B. abortus isolate that included simultaneous resistance to cefoperazone, rifampicin, and trimethoprim/sulfamethoxazole. The high susceptibility profiles we found against to antibiotics such as tetracycline, doxycycline gentamicin and ciprofloxacin, used widely in treatment, are encouraging. However, the change in the canonical Brucella species-primary host preference suggests the need to reconsider eradication program, including updating vaccine formulations.