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Importance of antimicrobial susceptibility testing for the management of eradication in Helicobacter pylori infection

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World Journal of gastroenterology 2017年第16期23卷 2854-2869页

作者： Nazli Arslan ozlem Yilmaz ebru demiray-gürbüz Department of Medical Microbiology Faculty of MedicineDokuz Eylül UniversityInciraltiIzmir 35340Turkey

The management of Helicobacter pylori(H. pylori) infection treatment differs from the common treatment protocol for other infectious diseases. Because culture-or molecular-guided approaches face several practical issues, such as the invasive procedures required to obtain gastric biopsy specimens and the lack of availability of routine laboratory testing in some places, H. pylori treatment includes the administration of two or three empirically selected antibiotics combined with a proton pump inhibitor rather than evidence-based eradication treatment. The efficacy of empirical therapy is decreasing, mostly due to increasing multiple resistance. Multiresistance to levofloxacin, clarithromycin, and metronidazole, which are commonly used in empirical treatments, appears to have increased in many countries. Mutations play a primary role in the antimicrobial resistance of H. pylori, but many different mechanisms can be involved in the development of antibiotic resistance. Determining and understanding these possible mechanisms might allow the development of new methods for the detection of H. pylori and the determination of antimicrobial resistance. A treatment based on the detection of antimicrobial resistance is usually more effective than empirical treatment. Nevertheless, such an approach before treatment is still not recommended in the Maastricht guidelines due to the difficulty associated with the routine application of available cultureor molecular-based susceptibility tests, which are usually administered in cases of treatment failure. The management of first and rescue treatments requires further research due to the steadily increase in antimicrobial resistance.

关键词： Helicobacter pylori Antimicrobial resistance Antimicrobial susceptibility testing Susceptibility-guided therapy Treatment management

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Clinical role and importance of fluorescence in situ hybridization method in diagnosis of H pylori infection and determination of clarithromycin resistance in H pylori eradication therapy

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World Journal of gastroenterology 2007年第5期13卷 671-675页

作者： zlem Yilmaz ebru demiray Dokuz Eylül University Faculty of Medicine Department of Microbiology and Clinical Microbiology 35340 Inciralt1-IZMIR Turkey

H pylori is etiologically associated with gastritis, gas-tric and duodenal ulcers, gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. Eradicating H pylori may convert rapidly the outcome of related diseases with the use of more accurate diagnostic molecular tests. Indeed some of the tests cannot give the evidence of current infection; H pylori can be detected by noninvasive and invasive methods, the latter requiring an endoscopy. Eradication failure is a big problem in H pylori infection. Recently, clarithromycin resistance in H pylori strains is increasing and eradicati-on therapy of this bacterium is becoming more difficult. Molecular methods have frequently been applied besides phenotypic methods for susceptibility testing to detect clarithromycin resistance due to mutations in the 2143 and 2144 positions of 23S rRNA gene. Fluorescence in situ hybridization (FISH) method on paraffin embedded tissue is a rapid, accurate and cost-effective method for the detection of H pylori infection and to determine clarithromycin resistance within three hours according to the gold standards as a non-culture method. This method can also be applied to fresh biopsy samples and the isolated colonies from a culture of H pylori, detecting both the culturable bacillary forms and the coccoid forms of H pylori, besides the paraffin embedded tissue secti-ons. This technique is helpful for determining the bac-terial density and the results of treatment where clarith-romycin has been widely used in populations to increase the efficacy of the treatment and to clarify the treatment failure in vitro.

关键词： H pylori Fluorescence in situ hybridization method Clarithromycin resistance

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Comparison of invasive methods and two different stool antigen tests for diagnosis of H pylori infection in patients with gastric bleeding

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World Journal of gastroenterology 2006年第26期12卷 4206-4210页

作者： ebru demiray zlem Yilmaz Cihat Sarkis Müjde Soytürk lkay ■im■ek Department of Microbiology and Clinical Microbiology Faculty of Medicine Dokuz Eylül UniversityInciralti 35340 IzmirTurkey Department of gastroenterology Faculty of Medicine Dokuz Eylül UniversityInciralti 35340 IzmirTurkey

AIM： To compare two different H pylori stool antigen tests as noninvasive diagnostic methods. METHODS： The study population consisted of 22 upper gastrointestinal system bleeding patients. Urea breath test （UBT）, rapid urease test （RUT） and histopathological examination were applied to all patients. Stool specimens from these patients were examined by rapid STPIP!HpSA and one step simple H pylori antigen cassette test for the detection of Hpylori antigens. RESULTS： For these 22 patients, 15 （68.2%） were diagnosed as positive and seven （31.8%） were diagnosed negative for H pylori infection by the gold standard methods. Whereas 10 （45.5%） were positive and 12 （54.5%） were diagnosed negative by the rapid STPIP!HpSA test. The sensitivity, specificity, positive and negative predictive values were 60%, 86%, 90% and 50%, respectively. When compared to the gold standard methods, these differences were not significant. However, six patients （27.3%） were positive, and 16 （72.7%） were negative by the simple H pylori stool antigen cassette test. The sensitivity, specificity, positive and negative predictive values were 33%, 86%, 83% and 38%, respectively. Compared to the gold standard methods, the simple H pylori stool antigen cassette test results were significantly different （P = 0.012）. CONCLUSION： Rapid STRIP!HpSA test could be used as a routine diagnostic tool in the microbiology laboratory for assessing clinical significance and eradication control of H pylori in upper gastrointestinal system bleeding patients.

关键词： H pylori Stool antigen test Rapid STRIP!HpSA Simple Hpylori antigen cassette test

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Bench-top aqueous two-phase extraction of isolated individual single-walled carbon nanotubes

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Nano Research 2015年第5期8卷 1755-1769页

作者： Navaneetha K. Subbaiyan A. Nicholas g. Parra-Vasquezt Sofie Cambre Miguel A. Santiago Cordoba Sibel ebru Yalcin Christopher E. Hamilton Nathan H. Mack Jeffrey L. Blackburn Stephen K. Doorn Juan g. Duque Chemistry Division Physical Chemistry and Applied Spectroscopy Group (C-PCS) Center for Integrated Nanotechnologies (CINT) and Materials Science & Technology Division (MST-7) Los Alamos National Laboratory Los Alamos New Mexico 87544 USA Experimental Condensed Matter Physics Laboratory University of Antwerp Antwerp B-2610 Belgium National Renewable Energy Laboratory Golden Colorado 80401 USA

Isolation and purification of single-walled carbon nanotubes （SWCNTs） are prerequisites for their implementation in various applications. In this work, we present a fast （-5 min）, low-cost, and easily scalable bench-top approach to the extraction of high-quality isolated SWCNTs from bundles and impurities in an aqueous dispersion. The extraction procedure, based on aqueous two-phase （ATP） separation, is widely applicable to any SWCNT source （tested on samples up to 1.7 nm in diameter） and independent of defect density, purity, diameter, and length. The extracted dispersions demonstrate that the removal of large aggregates, small bundles, and impurities is comparable to that by density gradient ultracentrifugation, but without the need for high-end instrumentation. Raman and fluorescence-excitation spectroscopy, single-nanotube fluorescence imaging, atomic force and transmission electron microscopy, and thermogravimetric analysis all confirm the high purity of the isolated SWCNTs. By predispersing the SWCNTs without sonication （only gentle stirring）, full-length, pristine SWCNTs can be isolated （tested up to 20 μm）. Hence, this simple ATP method will find immediate application in the generation of SWCNT materials for all levels of nanotube research and applications, from fundamental studies to high-performance devices.

关键词： carbon nanotubes aqueous two-phase (ATP)separation aggregate removal isolation sorting

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伊斯坦布尔

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2018年

作者：埃布鲁·宝雅(ebru Boyar)，凯特·弗利特(Kate Fleet)

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Pistachio genomes provide insights into nut tree domestication and zW sex chromosome evolution

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Plant Communications 2023年第3期4卷 80-98页

作者： Salih Kafkas Xiaokai Ma Xingtan zhang Hayat Topc¸u Rafael Navajas-Pérez Ching Man Wai Haibao Tang Xuming Xu Mortaza Khodaeiaminjan Murat güney Aibibula Paizila Harun Karcı Xiaodan zhang Jing Lin Han Lin Roberto de la Herrán Carmelo Ruiz Rejón Jerson Alexander garcía-zea Francisca Robles Coral del Val Muñoz Agnes Hotz-Wagenblatt Xiangjia Jack Min HakanÖzkan Elmira ziya Motalebipour Hatice gozel Nergiz C¸oban Nesibe ebru Kafkas Andrej Kilian HuaXing Huang Xuanrui Lv Kunpeng Liu Qilin Hu Ewelina Jacygrad William Palmer Richard Michelmore Ray Ming Department of Horticulture Faculty of AgricultureUniversity of C¸ukurovaAdana 01330Turkey Center for genomics and Biotechnology Haixia Institute of Science and TechnologySchool of Future TechnologyFujian Agriculture and Forestry UniversityFuzhouChina Key Laboratory of Orchid Conservation and Utilization of National Forestry and grassland Administration Fujian Agriculture and Forestry UniversityFuzhouChina Departamento de genética Facultad de CienciasCampus de Fuentenueva s/n18071 GranadaSpain Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and EcologyXiamen UniversityXiamen 361102China Department of Computer Science University of GranadaGranadaSpain Andalusian Research Institute in Data Science and Computational Intelligence(DaSCI Institute) 18014 GranadaSpain german Cancer Research Center Omics IT and Data Management Core FacilityHeidelbergGermany Department of Biological Sciences Youngstown State UniversityYoungstownOH 44555USA Department of Field Crops Faculty of AgricultureUniversity of C¸ukurovaAdana 01330Turkey Pistachio Research Institute SxahinbeyGaziantep 27060Turkey Diversity Arrays Technology University of CanberraCanberraACTAustralia genome Center University of California Davis451 Health Sciences DriveDavisCA 95616USA

Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with zW sex *** sequenced the genomes of Pistacia vera cultivar(cv.)Siirt,the female parent,and *** ***,the male *** chromosome-level reference genomes of pistachio were generated,and z and W chromosomes were *** zW chromosomes originated from an autosome following the first inversion,which occurred approximately 8.18 *** inversion events in the W chromosome led to the formation of a 12.7-Mb(22.8%of the W chromosome)non-recombining *** W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a zW sex chromosome system in *** W-specific genes,including defA,defA-like,DYT1,two PTEN1,and two tandem duplications of six VPS13A paralogs,are strong candidates for sex determination or *** history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago,dating the domestication event close to the archeological record of pistachio domestication in *** identified 390,211,and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality,grafting success,flowering time shift,and drought *** findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

关键词： Pistacia vera pistachio sequencing reference genome sex chromosome domestication

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