Fatih Köksal - Academia.edu (original) (raw)

Papers by Fatih Köksal

Annals of Microbiology and Infectious Diseases

IntroductIon Escherichia coli (E. coli) is the commonest member of the Gram-negative bacteria fam... more IntroductIon Escherichia coli (E. coli) is the commonest member of the Gram-negative bacteria family of Enterobacteriaceae, which was identified by Theodor Escherich.[1,11] This non-spore forming and generally motile (with a peritrichous flagellated arrangement), facultative anaerobic rod-shaped bacteria were named E. coli by the suggestion of Castellani and Chalmers in 1919 [2, 3, 4]. There are a diversity of E. coli strains, which are divided into commensal types (intra-intestinal non-pathogenic strains) and pathotypes (intra-intestinal pathogenic E. coli (InPEC) and extra-intestinal pathogenic E. coli (ExPEC)). The commensal types of E. coli are able to be settled within the infants' alimentary canal, just in few hours after birth as beneficial normal microbialpopulation [5, 6]. ExPEC strains are gram-negative bacteria, which are isolated from urinary tract infections (UTI), newborn meningitis, sepsis, hospital-based pneumonia, osteomyelitis and the likes, are among the leading causes of mortality and morbidity [7,8]. In this study, we aimed to determine the effectiveness of RAPD and PFGE methods in order to shed lights into epidemiologic studies.The study was designed to find whether special genotypes are mutated or random mutations bring about the virulence characteristics of ExPEC strains. If this mutation can change the genes to pathogenicin gut microbiota, even though they are commensalinthe intestinal system [9,10].

Biomedical Research-tokyo, 2017

Objective(s): Helicobacter pylori are gastric infectious agents that colonizes majority of the wo... more Objective(s): Helicobacter pylori are gastric infectious agents that colonizes majority of the world's population. Genetic diversity among the virulence factors of bacterium like cytotoxin associated gene Pathogenicity Island (cagPAI) and vacuolating cytotoxinA (vacA) could have a modifying result on the pathogenic potential of the infecting strain. This study aimed to analyse which genes can be recommended as doubtless related virulence factors for H. pylori associated active chronic gastritis and stomach adenocarcinoma in Iranian and Turkish population. Material and methods: We tend to targeted on some cag PAI components and vacA gene subtypes based on correlations shown in some previous studies. So as to realize our goal, formalin fixed Paraffin Embedded (FFPE) tissues obtained from Iranian and Turkish patients. The prevalence of the cagPAI and vacA genotypes were studied in H. pylori positive samples by using Polymerase Chain Reaction (PCR) technique and specific primers. Results: From all of 320 patients, H. pylori were detected in 28.43% of patients. We tend to found that vacAs1, vacAm2 and cagA genes with mean prevalence of 82.41%, 71.42% and 69.23% were dominant in both of Iranian and Turkish patients. Conclusion: Finally in Turkish and Iranian population the genes that were studied, was homogeneous and there's no important variations in bacterial genetic and with the exception of H. pylori infection different factors like host genetic and nourishment play a crucial role within the formation of gastric cancer. However it's attainable that if statistical population will increase, the cagA gene association with cancer are going to be meaningful.

African Journal of Microbiology Research, Feb 12, 2013

The aim of this study was to investigate the frequency of CTX-M type extended-spectrum betalactam... more The aim of this study was to investigate the frequency of CTX-M type extended-spectrum betalactamase (ESBL)-producing Escherichia coli strains which have become emerging etiologic agents of urinary tract infections (UTIs). A total of 310 E. coli isolates recovered from UTIs were screened for ESBL production by VITEK2 system and the double-disk synergy tests. In addition, ESBL positive isolates were selected for typing of bla CTX-M genes by PCR screening followed by DNA sequencing analysis permitting the differentiation of the CTX-M subtypes. A pulsed-field gel electrophoresis (PFGE) assay was also performed to check for a possible clonal relation among these isolates. ESBL positivity was detected in 77 (24.8%) of isolates. Subsequently, 46 (14.8%) of ESBL positive E. coli isolates were shown to be carrying bla CTX-M genes of which 30 (9.6%) were found to be CTX-M-15 producers, while the remaining 16 (5.1%) were CTX-M-14 producers. No major clonal relationship among these bla CTX-M producers was found. We demonstrated the presence of CTX-M-14 producer E. coli strains for the first time in Turkey and provided epidemiologic data suggesting the evidence for the ongoing dissemination of CTX-M type ESBLs.

Flora the Journal of Infectious Diseases and Clinical Microbiology

Giriş: Komplike cerrahi uygulanması sebebiyle görülen ağır abdominal sepsis olgularında kaynak ko... more Giriş: Komplike cerrahi uygulanması sebebiyle görülen ağır abdominal sepsis olgularında kaynak kontrolü ile birlikte erken ve etkili antimikrobiyal tedavi hayat kurtarıcıdır. Bu çalışmada hastanemizde intra-abdominal infeksiyonlu hastalardan sekonder ve tersiyer peritonit etkeni olarak izole edilen gram-negatif bakterilerin antibiyotik direnç paternlerinin tespiti ve aralarındaki filogenetik ilişkinin belirlenmesi amaçlandı. Materyal ve Metod: Çukurova Üniversitesi Balcalı Hastanesinin Genel Cerrahi Servisinde ve Cerrahi Yoğun Bakım Ünitesinde sekonder ve tersiyer peritonit klinik tanısı ile yatarak takip edilen ardışık hastalar iki grup halinde incelendi. Birinci grubu başka bir hastanede, ikinci grubu ise hastanemizde opere edilen hastalar oluşturdu. İzolatların tür düzeyinde identifikasyonu ve antibiyotik direnç paternlerinin tespiti VITEK-2 otomatize sistemle yapıldı. Suşlar arasındaki akrabalık ilişkisi Pulsed-Field Gel Elektroforezi (PFGE) yöntemi ile belirlendi.

Mikrobiyoloji Bulteni, Jan 9, 2023

Etambutol (EMB), Mycobacterium tuberculosis kompleksi (MTC)'nin neden olduğu tüberküloz (TB) hast... more Etambutol (EMB), Mycobacterium tuberculosis kompleksi (MTC)'nin neden olduğu tüberküloz (TB) hastalığının standart kombinasyon tedavisinde kullanılan birinci seçenek ilaçlardan biridir ve tedavide anahtar rol oynayan ilaçlara karşı direnç dünya genelinde artmaktadır. EMB direncinden, embCAB operonundaki dirençle ilişkisi doğrulanmış mutasyonlar sorumlu tutulmaktadır. Bu çalışmada, fenotipik olarak EMB'ye dirençli ve duyarlı olduğu saptanan klinik MTC izolatlarında embA, embB ve embC gen bölgelerinde meydana gelen mutasyonların sıklığının ve paternlerinin belirlenmesi amaçlanmıştır. Çalışmaya geleneksel fenotipik ilaç duyarlılık testi ile EMB dirençli 44 ve EMB, izoniyazid, rifampisin ve streptomisine duyarlı 20 olmak üzere toplamda 64 adet MTC izolatı dahil edilmiştir. DNA izolasyonu sonrası, EMB direnci ile ilişkili embA, embB ve embC gen bölgeleri özgül primer dizileri ile amplifiye edilmiştir. Elde edilen PCR amplifikasyon ürünleri, 'Bigdye Terminator v3.1 Cycle Sequencing kit' (Applied Biosystems, ABD) kullanılarak döngü dizileme yapılmıştır. Reaksiyon ürünlerinin elektroforez işlemi ABI PRISM 3130XL Genetic Analyzer (Applied Biosystems, ABD) otomatize DNA dizi analizi cihazında gerçekleştirilmiştir. Dizi analizi verileri çoklu dizi analiz programlarında hizalanarak mutasyona uğramış gen bölgeleri belirlenmiştir. Çalışmada EMB dirençli izolatların %68.2 (30/44)'sinde embCAB operonunda genomik mutasyonlar

Annals of Microbiology, 2010

A clinical isolate of Enterobacter cloacae BF280 showing a multidrug resistance phenotype includi... more A clinical isolate of Enterobacter cloacae BF280 showing a multidrug resistance phenotype including resistance to β-lactams and quinolones is the subject of this study. This strain was isolated from a patient at the intensive care unit of a military hospital (hôpital Militaire de Tunis). By polymerase chain reaction amplification and sequencing, this isolate was found to produce quinolone resistance determinant QnrS1. In addition, it was found to produce CTX-M-28, OXA-1 and TEM-1. The qnrS, bla CTX-M-28 , bla TEM-1 and bla OXA-1 genes were located on a highly conjugative plasmid.

DergiPark (Istanbul University), Mar 1, 1996

Journal of Clinical Medicine of Kazakhstan

Aim: This study aimed to determine the susceptibility of carbapenem-resistant Gr (-) bacilli isol... more Aim: This study aimed to determine the susceptibility of carbapenem-resistant Gr (-) bacilli isolated from various clinical infections to various antibiotics and identify genes causing carbapenem resistance and their clonal relationships to elucidate the distribution of resistance in community and/or hospital-acquired strains. Material and methods: In this study, antibiotic susceptibilities of 450 carbapenem-resistant Gr (-) bacilli isolated from clinical specimens at Cukurova University, Faculty of Medicine, Balcali Hospital, were investigated using phenotypic methods. The presence of carbapenems and β-lactamase genes were searched using polymerase chain reaction (PCR) and sequence analysis methods. Pulsed-field gel electrophoresis (PFGE) method was used to evaluate the phylogenetic relationship of the isolates. Results: Based on the results, it was determined that 99.23% of the strains had gained resistance to meropenem, whereas 5.38% had developed resistance to colistin. The most...

Iranian Journal of Public Health

Background: The adeABC efflux pump has a crucial role in the resistance of Acinetobacter baumanni... more Background: The adeABC efflux pump has a crucial role in the resistance of Acinetobacter baumannii strains to antimicrobial agents; it is encoded by adeABC, adeR, adeS genes. We evaluated antibiotic resistance, efflux pump genes, clonal relationships, and analyzed a probable correlation that can exist between antibiotic resistance and the aforementioned genes. Methods: We conducted this study on 27 food-originated and 50 human clinical Acinetobacter spp. in Southern Türkiye. MALDI-TOF system and disc diffusion/agar dilution (colistin) methods were used for the identification and antibiotic susceptibility. The efflux pump genes and genetic relatedness of the two groups were investigated by (PCR) and (PFGE) methods. Results: Foodborne A. dijkshoorniae strain was multidrug- resistant (MDR), and none of them resistant to colistin. Most of the clinical isolates (92%) were Extensive-Drug Resistant (XDR); highest resistant to ceftazidime, piperacillin-tazobactam, and imipenem (47, 94%), an...

Kahramanmaraş Sütçü İmam Üniversitesi Tıp Fakültesi Dergisi, 2020

Bakteriyel vajinosis (BV) puberte dönemindeki kadınlarda en sık görülen alt genital sistem yakınm... more Bakteriyel vajinosis (BV) puberte dönemindeki kadınlarda en sık görülen alt genital sistem yakınmasıdır. Vajendeki ekosistemin bozulması sonucu koruyucu laktobasillerin azalması ve anaerob bakteri sayısının aşırı derecede artması sonucu ortaya çıkar. Bu çalışmada asemptomatik 40 kadından alınan vajinal (VSÖ) ve rektal sürüntü örnekleri (RSÖ) laktobasil insidansı ve türlerinin dağılımını tespit için sellektif kültür yöntemleri kullanılarak değerlendirilmiştir. Ayrıca laktobasillerin karekterizasyonunda fenotipik yöntemlerin yanı sıra sekans bazlı RAPD-PCR yöntemi denenmiştir. Çalışmaya dahil edilen kadınların Ison & Hay kriterlerine göre değerlendirilmesi sonucu 5 (%15)’inin asemptomatik BV bulgularına sahip oldukları görülmüştür. Kadınların vajen ve rektum sürüntü örneklerinden 132 farklı bakteri kolonisi laktobasil şüpheli bulunmuş, kristal yöntemi ile bunlardan 111’inin 11 farklı türe ait laktobasil olduğu, RAPD-PCR ile yapılan tiplendirmede ise sadece 101’inin 9 farklı tür laktob...

A peptic ulcer is an ulcer of one of those areas of the gastrointestinal tract that are usually a... more A peptic ulcer is an ulcer of one of those areas of the gastrointestinal tract that are usually acidic. Peptic ulcer formation occurred due to the acid of excess, peptic activity in gastric juice as well as a breakdown in mucosal defenses. Some of anti-ulcer medicines such as proton pump inhibitors and H2 receptor antagonists are used for peptic ulcer treatment. However, these drugs have shown disease relapse, side effects, and even drug interactions. Many medicinal plants exhibit anti-ulcer activity and found useful in the treatment of peptic ulcer. The purpose of this review is to know more about the anti-ulcer properties of the medicinal plants. Serjania marginata (HESM) leaves, thymol obtained from Thymus, Origanum and Cuphea aequipetala infusion (CAI) In this review there is information about some kinds of plants which are very useful in treating peptic ulcer disease such as hydroalcoholic extract obtained from S. marginata (HESM) leaves, thymol obtained from Thymus, Origanum a...

Calismanin hedefi hastanemiz yanik unitesinde gorulen Acinetobacter baumannii salgininin kaynagin... more Calismanin hedefi hastanemiz yanik unitesinde gorulen Acinetobacter baumannii salgininin kaynaginin, mekanizma- sinin ve kontrol stratejisinin basarisinin irdelenmesidir. Ayni birimdeki bir onceki salginda bir klinik ornekten izole edilen ve "indeks sus" olarak adlandirilan 3 yillik susa ek olarak yanik unitesinde cevresel orneklerden izole edilen karbapenemlere direncli 11 A.baumannii susu calismaya alinmistir. Izolatlar fenotipik olarak tani konduktan sonra OXA tipi beta-laktamaz genlerinin tanimlanmasi icin tip-spesifik-multipleks-PCR yontemi ile calisilmistir. Suslar arasindaki klonal iliskiler PFGE yontemi ile arastirilmistir. Indeks sus da dahil butun izolatlar karbapenem direncli bulunmustur. blaOXA-51-like geni butun izolatlarda tespit edilirken 3 susta blaOXA-51-like genine ek olarak blaOXA-24-like geni de tespit edilmistir. PFGE calismasi sonunda izolatlar 2 yakin iliskili alt-grub icerisinde yer almistir ve indeks susun da en kalabalik grubla % 100 iliskili oldu...

Çukurova Üniversitesi Tıp Fakültesi dergisi, 1996

Background: Determinants of extraintestinal infection in Escherichia coli (E. coli) remain unclea... more Background: Determinants of extraintestinal infection in Escherichia coli (E. coli) remain unclear. Virulence factors making Extraintestinal pathogenic E. coli (ExPEC) different from other E. coli strains are the host cell adhesion, invasion, and two important factors/toxins, Cytotoxic Necrotizing Factor (CNF) and Cytolethal Distending Toxin (CDT) that are responsible for cell death. In the present study, prevalence of CNF-CDT genotypes was investigated in 645 E. coli strains isolated from patients. This prevalence was analyzed regarding clinical origins, phylogroups and putative phylogenetic relationships.Results: At least one virulence gene identified for ExPEC was found in 156 (24%) of 645 E. coli strains. 78, 12, 20 of ExPEC strains contained cnf1, cnf2, cnf3, respectively. Genes of cdt1, cdt2, cdt3 and cdt4 were detected as 20, 4, 4, 4. Finally, two factors were detected cnf1-cnf3 (n=6), cnf1- cdt1 (n=4), cdt1-cdt4 (n=4). These 156 strains were found to be distributed in 106 la...

Amac: Akciger tuberkulozunun teshisi balgamin bakteriyolojik tetkiki ile mumkundur. Balgam yaymal... more Amac: Akciger tuberkulozunun teshisi balgamin bakteriyolojik tetkiki ile mumkundur. Balgam yaymalarin mikroskobik incelemesi etkilidir ve hastaligi dogrular. Fakat Balgam yaymalarin mikroskobik incelemesinin duyarliligi dusuktur. Calismamizda balgamdan Direkt yaymayla (DS) yapilan preparatlarin Modifiye– auramine flourokrom boyama (MR-AFS) yontemiyle aside direncli basillerin (AFB) boyanmasinin kullanisli oldugunu gostermeyi amacladik. Hastalar ve Yontem: Toplam 218 hastadan 10 pozitif kontrol ve 10 negatif kontrolden alinan AFB’in MR-AFS ve Ziehl-Neelsen Boyama ZNS yontemleri ile BACTEC TB sistem altin standard olarak kabul edilerek incelendi ve kiyaslandilar. Bulgular: BACTEC TB sistemi ile 16 ornek, 13 ornek MR-AFS yontemi ile ve 11 ornek ZNS AFS yontemi ile pozitif olarak tespit edilmistir. Pozitif olarak tespit edilen orneklerin oranlari ZNS yonteminde MR-AFS yontemine gore belirgin olarak yuksek olarak bulunmustur (p < 0.01). BACTEC TB sistem altin standard olarak kabul edi...

New Microbes and New Infections, 2019

The aim of this study was to describe the epidemiological data, clinical features and outcome of ... more The aim of this study was to describe the epidemiological data, clinical features and outcome of patients with Elizabethkingia meningoseptica bacteraemia and to report the antimicrobial susceptibility pattern. All patients with E. meningoseptica bacteraemia were retrospectively

Current Molecular Pharmacology, 2019

Background:Mycobacterium tuberculosis (Mtb) is considered as one of the most efficacious human pa... more Background:Mycobacterium tuberculosis (Mtb) is considered as one of the most efficacious human pathogens. The global mortality rate of TB stands at approximately 2 million, while about 8 to 10 million active new cases are documented yearly. It is, therefore, a priority to develop vaccines that will prevent active TB. The vaccines currently used for the management of TB can only proffer a certain level of protection against meningitis, TB, and other forms of disseminated TB in children; however, their effectiveness against pulmonary TB varies and cannot provide life-long protective immunity. Based on these reasons, more efforts are channeled towards the development of new TB vaccines. During the development of TB vaccines, a major challenge has always been the lack of diversity in both the antigens contained in TB vaccines and the immune responses of the TB sufferers. Current efforts are channeled on widening both the range of antigens selection and the range of immune response elici...

Turkiye Klinikleri Journal of Gynecology and Obstetrics, 1991

Ankara Üniversitesi Veteriner Fakültesi Dergisi, 2014

The aims of this research were to study the prevalence of potential virulence factors, vancomycin... more The aims of this research were to study the prevalence of potential virulence factors, vancomycin resistance and also to evaluate a possible correlation that can exist between vancomycin resistance and potential virulence factors between 51 Enterococcus spp. isolated from food and 50 Enterococcus faecium strains from human in southern Turkey. Identification of the isolates was determined by Vitek-II system. Antimicrobial susceptibility tests were performed by Vitek-II system and disc diffusion method. The presence of vanA and vanB as well as enterococcal virulence genes of cytolysin (cylA), the aggregation substance (asa1), gelatinase (gelE), enterococal surface protein (esp), hyaluronidase (hyl) were investigated by Polymerase Chain Reaction (PCR) method. Haemolysin production was also studied phenotypic method. Apart from one isolate, none of the food originated enterococci were resistant to vancomycin, and none carried vanA and vanB resistance genes. All clinical isolates were resistant to vancomycin and 84% of them carried vanA; 2%, vanB; and 14%, neither vanA nor vanB genes. Except for the cylA gene, all other virulence genes and vancomycin resistance were higher in human strains, and a positive correlation was observed between multivirulence genes and hemolytic activity. For all strains, a positive correlation existed between the esp gene positivity and vancomycin resistance, while for only E. faecium, esp, hyl gene positivity and vancomycin resistance a positive correlation could be seen. Furthermore, "silent cylA" genes were found in two food and one intestinal strains. Based on our findings, we can suggest that virulence increases in parallel to vancomycin resistance, and food may be a potential source for dissemination of gelE, asa1 and hyl virulence genes. Finally, esp and hyl genes presence should carefully be monitored in food originated enterococci.

Journal of Clinical and Experimental Dentistry, 2012

Aim: The aim of this study was to determine the frequency of two important pathogenic microorgani... more Aim: The aim of this study was to determine the frequency of two important pathogenic microorganisms associated with endodontic infections, Enterococcus faecalis and Candida albicans, in root canal samples from patients with necrotic pulps or failed canal therapy by polymerase chain reaction method. Method: Microbial samples were obtained from 117 teeth with necrotic pulp tissues and 114 teeth with failed endodontic treatment. Results: E.faecalis were identified in 16% of the necrotic and 10% of the retreated root canal infections by PCR. C.albicans genome were identified in 20% and 11% of the necrotic and retreated root canal infections, respectively, by PCR. The frequencies of microbiota were not statistically different between necrotic and retreatment groups (p > 0.05, chi squared test). Conclusions: PCR analysis of teeth with periapical lesions revealed that E.faecalis was found in fewer patients than in previous studies. The C.albicans prevelance was consistent with previous reports. No statistical difference was found between primary and secondary root canal infections for C.albicans or E.faecalis.