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Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

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Genomics, Proteomics & Bioinformatics 2019年第2期17卷 169-182页

作者： Valentina Galata Cédric C. Laczny Christina Backes Georg Hemmrich-Stanisak Susanne Schmolke Andre Franke Eckart Meese Mathias Herrmann Lutz von Müller Achim Plum Rolf Mü ller Cord Stahler Andreas E. Posch Andreas Keller Chair for Clinical Bioinformatics Saarland University 66123 Saarbrücken Germany Helmholtz Center for Infection Research and Pharmaceutical Biotechnology (HZI) Saarland University 66123 Saarbrücken Germany institute of Clinical Molecular Biology Christian-Albrechts University of Kiel 24105 Kiel Germany Siemens Healthcare GmbH Strategy and Innovation 91052 Erlangen Germany Department of Human Genetics Saarland University 66421 Homburg Germany institute of medical microbiology and hygiene Saarland University 66421 Homburg Germany Ares Genetics GmbH 1030 Vienna Austria Curetis GmbH 71088 Holzgerlingen Germany Department of Pharmacy Pharmaceutical Biotechnology Saarland University 66123 Saarbrücken Germany Department of Microbial Natural Products Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Saarland University 66123 Saarbrücken Germany

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species,including conserved essential genes and known resis-tance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base,a resource available for academic research use free of charge at https://***.

关键词： Antibiotic resistance Whole-genome sequencing Bacteria Pan-genome

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Revision of genera in Asterinales

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Fungal Diversity 2014年第5期68卷 1-68页

作者： Sinang Hongsanan Yan-Mei Li Jian-Kui Liu Tina Hofmann Meike Piepenbring Jayarama D.Bhat Saranyaphat Boonmee Mingkhuan Doilom Chonticha Singtripop Qing Tian Ausana Mapook Xiang-Yu Zeng Ali H.Bahkali Jian-Chu Xu Peter E.Mortimer Xia-Hai Wu Jun-Bo Yang Kevin D.Hyde Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China institute of Excellence in Fungal Research Chiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry Centre East Asia NodeHeilongtanKunming 650201People’s Republic of China International Fungal Research and Development Centre Key Laboratory of Resource Insect Cultivation and Utilization State Forestry AdministrationKunmingPeople’s Republic of China Herbario UCH Centro de Investigaciones Micológicas(CIMi)Universidad Autónoma de Chiriquí0427 DavidChiriquíPanama Department of Mycology Institute of EcologyEvolutionand DiversityGoethe University Frankfurt am MainBiologicumMax-von-Laue-Str.1360438 Frankfurt am MainGermany Formerly at Department of Botany Goa UniversityGoa 403206India College of Science Botany and Microbiology DepartmentKing Saud UniversityRiyadh 1145Saudi Arabia Germplasm Bank of Wild Species in Southwest China Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina

The order Asterinales comprises a single family,*** this study,types or specimens of 41 genera of Asterinaceae are re-examined and re-described and illustrated by *** genera,namely Asterina(type genus),Asterinella,Asterotexis,Batistinula,Cirsosia,Echidnodella,Halbania,Lembosia,Meliolaster,Parasterinopsis,Platypeltella,Prillieuxina,Schenckiella(=Allothyrium),Trichasterina,Trichopeltospora,Uleothyrium and Vizellopsis,are maintained within ***,Lembosiella,Lembosina,Morenoina,and Thyriopsi s are transferred to Aulographaceae based on morphological and molecular *** is transferred to Micropeltidaceae,while Lembosiopsis is transferred to *** and Placosoma are morphologically close to taxa in Parmulariaceae,where they are *** is placed in Teratosphaeriaceae,while Asterodothis,Asterinema,Dothidasteromella,Leveillella,Petrakina and Stephanotheca are transferred to Dothideomycetes,genera incertae ***,Macowaniella,Maheshwaramyces,Parasterinella,and Vishnumyces are treated as doubtful genera,because of lack of morphological and molecular ***,Asterolibertia,Neostomella,Placoasterina,and Symphaster are synonyms of Asterina based on morphology,while Trichamelia,Viegasia,and Yamamotoa are synonyms of *** characteristics of each family are discussed and a phylogenetic tree is included.

关键词： Asterina Asterinaceae Aulographaceae Lembosiaceae morphology type species taxonomy

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氨氧化古菌的生态学研究进展

微生物学报 2010年第4期50卷 431-437页

作者：贾仲君翁佳华林先贵 Ralf Conrad 中国科学院土壤环境与污染修复重点实验室(南京土壤研究所) 南京210008 南京农业大学园艺学院南京210095 中国科学院南京土壤研究所土壤与农业可持续发展国家重点实验室南京210008 max Planek institute for Terrestrial microbiology Karl-von-Frisch-Strasse D-35043 Marburg Germany

上百年来细菌一直被认为是地球氨氧化过程的主要驱动者,2005年海洋中分离到迄今唯一的非极端环境泉古菌,发现其氧化氨态氮获得能源生长,是氨氧化古菌。氨氧化古菌和细菌对地球氨氧化过程的相对贡献率,是目前全球氮循环研究最重要的微生... 详细信息

上百年来细菌一直被认为是地球氨氧化过程的主要驱动者,2005年海洋中分离到迄今唯一的非极端环境泉古菌,发现其氧化氨态氮获得能源生长,是氨氧化古菌。氨氧化古菌和细菌对地球氨氧化过程的相对贡献率,是目前全球氮循环研究最重要的微生物生态学问题之一。已有的证据表明古菌在海洋氨氧化过程中发挥了重要作用,细菌则是土壤氨氧化过程的主要驱动者。本文重点探讨了原位自然环境下氨氧化古菌的生态学研究进展。

关键词：泉古菌(Crenarchaeota) 氨氧化古菌氨氧化 amoA基因微生物生态

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The quest for a globally comprehensible Russula language

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Fungal Diversity 2019年第6期99卷 369-449页

作者： Slavomır Adamcik Brian Looney Miroslav Cabon Sona Jancovicova Katarina Adamcikova Peter G.Avis Magdalena Barajas Rajendra P.Bhatt Adriana Corrales Kanad Das Felix Hampe Aniket Ghosh Genevieve Gates Ville Kalviainen Abdul Nasir Khalid Munazza Kiran Ruben De Lange Hyun Lee Young Woon Lim Alejandro Kong Cathrin Manz Clark Ovrebo Malka Saba Tero Taipale Annemieke Verbeken Komsit Wisitrassameewong Bart Buyck institute of Botany Plant Science and Biodiversity CenterSlovak Academy of SciencesDubravska cesta 984523 BratislavaSlovakia Department of Biology Duke University130 Science DriveDurhamNC 27708-0338USA Department of Botany Faculty of Natural SciencesComeniusUniversity in BratislavaRevova 3981102 BratislavaSlovakia Department of Plant Pathology and Mycology Institute of Forest EcologySlovak Academy of Sciences ZvolenAkademicka 294901 NitraSlovakia Indiana University Northwest 3400 BroadwayMarram HallRoom 308GaryIN 46408USA Department of Botany&microbiology H.N.B.Garhwal UniversityGarhwalSrinagar 246174UttarakhandIndia Programa de Biologia Facultad de Ciencias Naturales y MatematicasUniversidad del RosarioCr.24#63C-69BogotaD.C.Colombia A.J.C.Bose Indian Botanic Garden Botanical Survey of IndiaP.O.Botanic GardenHowrah 711103India Grafenroda Germany Tasmanian institute of Agriculture Private Bag 98HobartTAS 7001Australia Helsinki Finland Department of Botany University of the PunjabQuaid-e-Azam CampusLahore 54590Pakistan Department of Biology Ghent UniversityK.L.Ledeganckstraat 359000 GhentBelgium School of Biological Sciences and institute of microbiology Seoul National UniversitySeoul 08826South Korea Centro de Investigaciones en Ciencias Biologicas Km.10.5 Carretera San Martin Texmelucan-TlaxcalaCP.90120IxtacuixtlaTlaxcalaMexico Department of Mycology Goethe University Frankfurt am MainBiologicumMax-von-Laue-Str.1360438 Frankfurt am MainGermany Department of Biology University of Central Oklahoma100.N.University DriveBox 89EdmondOK 73034USA Department of Plant Sciences Quaid-i-Azam UniversityIslamabad 45320Pakistan Koskenkylan Saha Finland Institut de Systematique Ecologie et Biodiversite(ISYEB)Museum national d’histoire naturelleCNRSSorbonne UniversiteEPHE57 rue CuvierCP 3975005 ParisFrance

Since 2007,the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has ***,the description style is not consistent and has regional or author-specific *** recent publications still favour descriptions of spores compared to hymenium and pileipellis elements,and usually only the spore size is provided with statistical *** study proposes standards for descriptions of the microscopic structure of Russula species(Russulaceae,Agaricomycetes).We present the description template,the template measurements table,the specific terminology and the essential chemical *** proposed standards were tested by mycologists from 11 countries who met at the Russula Microscopy Workshop in *** of 26 species from 9 countries and four continents were prepared,among them ***,***,*** and *** are re-described and 15 species are introduced as new:***,***,***,***,***,***,***,***,***,***,***,***,***,***-pauli and *** descriptions for candidate new species are provided without a formal name *** comparison of species described in this study with available similar descriptions of related species suggests that microscopic characters from all parts of the basidiomata can be equally important for species recognition and they deserve the same treatment including number of measurements and *** majority of recent studies does not recognise differences between the pileus margin and centre,but more than one-third of the species described in this study show distinct differences between the pileus areas,emphasizing the importance to specify the origin of pileipellis *** study proved that there is frequently insufficient difference in the I

关键词： Morphology standards New species Phylogeny Species delimitation Taxonomy

应用第二代酶联免疫吸附法调查丙型肝炎在透析病人及接触者中的流行状况

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Oncology and Translational Medicine 1994年第2期11卷 121-121页

作者： U.Schlipkter U.Gladziwa K.Cholmakov A.Weise R.Rasshofer B.Lorbeer N.Luz F.Deinhardt M.Roggendorf 齐俊英 max v.pettenkofer-institute for hygiene and medical microbiology University of Munich Germany Hemodialysis Unit Medizinische Klinik University of Aachen Germany Himodialysis Unit Stdtisehes Krankenhaus Harlaching Munich Germany institute of Virology University of Essen Germany Hemodialysis Unit Stdtisehes Krankenhaus Amberg Germany 同济医科大学附属同济医院

透析病人血源性感染丙型肝炎且有高度的危险性。据报道在德国应用第一代酶联免疫吸附试验(ELISAA)检测抗 HCV 平均阳性率达10.1%(0%～37%)。本研究应用几种方法对来自德国三个透析中心的血透病人,医务人员及病人家属进行了抗HCV 检测。... 详细信息

透析病人血源性感染丙型肝炎且有高度的危险性。据报道在德国应用第一代酶联免疫吸附试验(ELISAA)检测抗 HCV 平均阳性率达10.1%(0%～37%)。本研究应用几种方法对来自德国三个透析中心的血透病人,医务人员及病人家属进行了抗HCV 检测。在498例血透病人中,应用针对非结构蛋白

关键词：透析病人 HCV 阳性率丙型肝炎病毒性肝炎 RIBA 第二代