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Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long-and Short-read Multi-metagenomic Sequencing Studies

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Genomics, Proteomics & Bioinformatics 2022年第2期20卷 405-417页

作者： Jacqueline Rehner Georges Pierre Schmartz Laura Groeger Jan Dastbaz Nicole Ludwig matthias Hannig Stefan Rupf Berthold Seitz Elias Flockerzi Tim Berger matthias christian.reichert Marcin Krawczyk Eckart Meese christian Herr Robert Bals Soren L.Becker Andreas Keller Rolf Muller The IMAGINE Consortium Institute of Medical Microbiology and Hygiene Saarland UniversityD-66421 HomburgGermany Clinical Bioinformatics Saarland UniversityD-66123 SaarbruckenGermany Department of Human Genetics Saarland UniversityD-66421 HomburgGermany Helmholtz Institute for Pharmaceutical Research Saarland D-66123 SaarbruckenGermany Clinic of Operative Dentistry Periodontology and Preventive DentistrySaarland UniversityD-66421 HomburgGermany Department of Ophthalmology Saarland University Medical CenterD-66421 HomburgGermany Department of Medicine Ⅱ Saarland University Medical CenterD-66421 HomburgGermany Department of Internal Medicine V–Pulmonology AllergologyIntensive Care MedicineSaarland UniversityD-66421 HomburgGermany

High-quality DNA extraction is a crucial step in metagenomic *** by different isolation kits impairs the comparison across datasets.A trending topic is,however,the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with *** thus collected bile,stool,saliva,plaque,sputum,and conjunctival swab samples and performed DNA extraction with three commercial *** each combination of the specimen type and DNA extraction kit,20-gigabase(Gb)metagenomic data were generated using short-read *** profiles of the specimen types showed close proximity to each other,we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction *** kit outperformed all selected kits on every *** reached consistently good results using the Qiagen QiAamp DNA Microbiome *** on the specimen,our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution,but DNA-based identification is superior to identification by mass ***,longread nanopore sequencing confirmed the results(correlation coefficient>0.98).Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

关键词： Whole-genome analysis Comparative genomics Short-read sequencing Long-read sequencing DNA extraction Metagenomics

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Retrospective study of the incidence, risk factors, treatment outcomes of bacterial infections at uncommon sites in cirrhotic patients

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World Journal of Hepatology 2024年第3期16卷 418-427页

作者： Sophie Schneitler Christina Schneider Markus Casper Frank Lammert Marcin Krawczyk Sören L Becker matthias christian.reichert Institute of Medical Microbiology and Hygiene Saarland UniversityHomburg 66421Germany Department of Medicine II Saarland University Medical CenterHomburg 66421Germany Health Sciences Hannover Medical SchoolHannover 30625Germany Laboratory of Metabolic Liver Diseases Department of GeneralTransplant and Liver SurgeryCentre for Preclinical ResearchMedical University of WarsawWarsaw 02-097Poland

BACKGROUND Bacterial infections(BI)negatively affect the natural course of *** most frequent BI are urinary tract infections(UTI),pneumonia,and spontaneousbacterial peritonitis(SBP).AIM To assess the relevance of bacterial infections beyond the commonly recognized types in patients with cirrhosis and to investigate their relationship with other clinical *** We retrospectively analyzed patients with cirrhosis and BI treated between 2015 and 2018 at our tertiary care *** were classified as typical and atypical,and clinical as well as laboratory parameters were compared between the two *** In a cohort of 488 patients with cirrhosis,we identified 225 typical BI(95 UTI,73 SBP,72 pulmonary infections)and 74 atypical BIs,predominantly cholangitis and soft tissue infections(21 each),followed by intra-abdominal BIs(n=9),cholecystitis(n=6),head/throat BIs(n=6),osteoarticular BIs(n=5),and endocarditis(n=3).We did not observe differences concerning age,sex,or etiology of cirrhosis in patients with typical vs atypical *** BIs were more common in patients with more advanced cirrhosis,as evidenced by Model of End Stage Liver Disease(15.1±7.4 vs 12.9±5.1;P=0.005)and Child-Pugh scores(8.6±2.5 vs 8.0±2;P=0.05).CONCLUSION Atypical BIs in cirrhosis patients exhibit a distinct spectrum and are associated with more advanced stages of the ***,the work-up of cirrhosis patients with suspected BI requires detailed work-up to elucidate whether typical BI can be identified.

关键词： Bacterial infection Empirical antibiotic therapy End-stage liver disease Escherichia coli Multi-resistant pathogens

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Evaluation of Ultrasound-based Surveillance for Hepatocellular Carcinoma in Patients at Risk:Results From a German Multicenter Retrospective Cohort Study

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Journal of Clinical and Translational Hepatology 2023年第3期11卷 626-637页

作者： Johannes Gillessen Philipp Reuken Peter-Marton Hunyady matthias christian.reichert Lucian Lothschütz Fabian Finkelmeier matthias Nowka Gabriel Allo Fabian Kütting Martin Bürger Dirk Nierhoff Hans-Michael Steffen Christoph Schramm University Hospital Cologne Department of Gastroenterology and HepatologyCologneGermany University Hospital Jena Department of Internal Medicine IV-GastroenterologyHepatologyInfectious DiseaseJenaGermany University Hospital Frankfurt Department of Internal Medicine 1-Gastroenterology und HepatologyPulmonology und AllergologyEndocrinologyFrankfurtGermany Department of Medicine II Saarland University Medical CenterHomburgGermany Department of Gastroenterology and Hepatology University Hospital of EssenEssenGermany

Background and Aims:Hepatocellular carcinoma(HCC)surveillance in patients at risk is strongly recommended and usually performed by ultrasound(US)semiannually with or without alfa-fetoprotein(AFP)*** pa-rameters except for surveillance intervals have not been strictly *** aimed to evaluate surveillance success and risk factors for surveillance ***:Patients with≥1 US prior to HCC diagnosis performed at four tertiary referral hospitals in Germany between 2008 and 2019 were retrospectively *** success was defined as HCC detection within Milan ***:Only 47%of 156 patients,median age 63(interquartile range:57-70)years,56%male,and 96%with cirrhosis,received recom-mended surveillance modality and *** fail-ure occurred in 29%and was significantly associated with lower median model for end-stage liver disease(MELD)score odds ratio(OR)1.154,95%confidence interval(CI):1.027-1.297,p=0.025)and HCC localization within right liver lobe(OR:6.083,95%CI:1.303-28.407,p=0.022),but not with AFP≥200μg/*** with surveillance failure had sig-nificantly more intermediate/advanced tumor stages(93%vs.6%,p<0.001),fewer curative treatment options(15%vs.75%,p<0.001)and lower survival at 1 year(54%vs.75%,p=0.041),2 years(32%vs.57%,p=0.019)and 5 years(0%vs.16%,p=0.009).Alcoholic and non-alcoholic fatty liver disease(OR:6.1,95%CI:1.7-21.3,p=0.005)and ascites(OR:3.9,95%CI:1.2-12.6,p=0.021)were in-dependently associated with severe visual limitations on ***:US-based HCC surveillance in patients at risk frequently fails and its failure is associated with unfavorable patient-related *** MELD score and HCC lo-calization within right liver lobe were significantly associated with surveillance failure.

关键词： Hepatocellular carcinoma Surveillance success Screening Ultra-sound.

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Indirect targeting of MYC sensitizes pancreatic cancer cells to mechanistic target of rapamycin (mTOR) inhibition

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Cancer Communications 2022年第4期42卷 360-364页

作者： christian Schneeweis Zonera HassanKatja Ascherl matthias Wirth Stella Koutsouli Felix Orben Lukas Krauß Carolin Schneider Rupert Ollinger Oliver HKrämer Roland Rad Maximilian reichert Maria SRobles Dieter Saur Günter Schneider Medical Clinic and Polyclinic II Klinikum rechts der IsarTechnical University MunichMunich 81675Germany Department of Hematology Oncology and Tumor ImmunologyCharite-Universitatsmedizin BerlinCorporate Member of Freie Universitat BerlinHumboldt-Universitat zu Berlin and Berlin Institute of HealthBerlin 12203Germany Institute of Medical Psychology and Biomedical Center(BMC) Faculty of MedicineLMU MunichMunich 80336Germany Institute of Molecular Oncology and Functional Genomics TUM School of MedicineTechnical University MunichMunich 81675Germany Department of Toxicology University of Mainz Medical CenterMainz 55131Germany German Cancer Research Center(DKFZ)and German Cancer Consortium(DKTK) Heidelberg 69120Germany Center for Protein Assemblies(CPA) Technical University of MunichGarching 85747Germany Institute for Translational Cancer Research and Experimental Cancer Therapy Technical University MunichMunich 81675Germany Department of General Visceral and Pediatric SurgeryUniversity Medical Center GottingenGottingen 37075Germany

Dear Editor,Pancreatic ductal adenocarcinoma(PDAC)remains a significant health problem with an increase in the incidence and a five-year survival rate of only 10%[1].The Phosphoinositide 3-kinase-protein kinase-B-mechanistic target of rapamycin(PI3K-AKT-mTOR)pathway is a driver pathway in PDAC and an important therapeutic target[2].We[3]and others[4–6]have demonstrated that the mTOR kinase is a therapeutic target in PDAC,and rationally designed mTOR inhibitor(mTORi)-based combination therapies are emerging[2].

关键词： rapamycin therapeutic adenocarcinoma

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越南河内国家会议中心(NCC)

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建筑技艺 2010年第7期16卷 40-47页

作者：曼哈德.冯.格康 Susi Winter Tuyen Tran Viet Robert Wildegger Hito Ueda Marcus Tanzen Udo Meyer Birgit Fllmer Jens reichert Uli Rsler Frederik Heisel Annika Schrder Elena Melnikova Markus Carlsen Nicole Flores Schlotfeldt Licht Müller BBM Breimann Bruun christian Gahl 德国gmp建筑师事务所越南国家建设咨询公司

会议中心、酒店和博物馆镶嵌在一片以越南文化和传统作为特色主题和象征的开阔的景观园林内。会议中心作为主导建筑坐落于南北轴线上,几乎占据了以大湖、小池和假山为特色的整个景观公园的中心地带。与园林景观的有机形状形成鲜明对比... 详细信息

会议中心、酒店和博物馆镶嵌在一片以越南文化和传统作为特色主题和象征的开阔的景观园林内。会议中心作为主导建筑坐落于南北轴线上,几乎占据了以大湖、小池和假山为特色的整个景观公园的中心地带。与园林景观的有机形状形成鲜明对比的是：道路和步道系统规划为一个严密的线性网格。

关键词：南河景观园林中心地带园林景观博物馆酒店建筑公园

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