Genome analysis of the novel putative rotavirus species K

Authors: Reimar Johne, Simon H. Tausch, Rainer G. Ulrich, Katja Schilling-Loeffler

Source: Virus Research, Vol 334, Iss , Pp 199171- (2023)

Subject Terms: Rotavirus, Genome sequence, Taxonomy, Phylogeny, Shrew, Microbiology, QR1-502, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S0168170223001338; https://doaj.org/toc/1872-7492

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Clonal relation between Salmonella enterica subspecies enterica serovar Dublin strains of bovine and food origin in Germany

Authors: Jörg Linde, Istvan Szabo, Simon H. Tausch, Carlus Deneke, Ulrich Methner

Source: Frontiers in Veterinary Science, Vol 10 (2023)

Subject Terms: whole-genome sequencing (WGS), Salmonella Dublin, cattle, food, bioinformatics, Veterinary medicine, SF600-1100

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fvets.2023.1081611/full; https://doaj.org/toc/2297-1769

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Typing methods based on whole genome sequencing data

Authors: Laura Uelze, Josephine Grützke, Maria Borowiak, Jens Andre Hammerl, Katharina Juraschek, Carlus Deneke, Simon H. Tausch, Burkhard Malorny

Source: One Health Outlook, Vol 2, Iss 1, Pp 1-19 (2020)

Subject Terms: Whole genome sequencing, Typing, Methods, Comparison, Bioinformatics tools, Environmental sciences, GE1-350, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s42522-020-0010-1; https://doaj.org/toc/2524-4655

Access URL: https://doaj.org/article/e727bc382b0c4f3fa85bfa948a43c920

Distantly Related Rotaviruses in Common Shrews, Germany, 2004–2014

Authors: Reimar Johne, Simon H. Tausch, Josephine Grützke, Alexander Falkenhagen, Corinna Patzina-Mehling, Martin Beer, Dirk Höper, Rainer G. Ulrich

Source: Emerging Infectious Diseases, Vol 25, Iss 12, Pp 2310-2314 (2019)

Subject Terms: rotavirus, shrews, common shrew, Sorex araneus, virus diversity, rotavirus A, Medicine, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://wwwnc.cdc.gov/eid/article/25/12/19-1225_article; https://doaj.org/toc/1080-6040; https://doaj.org/toc/1080-6059

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First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

Authors: Laura Uelze, Maria Borowiak, Carlus Deneke, Cécile Jacobs, István Szabó, Simon H. Tausch, Burkhard Malorny

Source: Gut Pathogens, Vol 11, Iss 1, Pp 1-8 (2019)

Subject Terms: Salmonella enterica subsp. diarizonae, Host-adaptation, Pseudogenes, Sheep, Diseases of the digestive system. Gastroenterology, RC799-869

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Relation: http://link.springer.com/article/10.1186/s13099-019-0330-9; https://doaj.org/toc/1757-4749

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Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST

Authors: Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny

Source: Frontiers in Microbiology, Vol 12 (2021)

Subject Terms: cgMLST, WGS typing, molecular surveillance, comparative microbial genomics, Salmonella, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.649517/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/774b28e00f8648fa96e188b27f44b066

PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets

Authors: Simon H. Tausch, Tobias P. Loka, Jakob M. Schulze, Andreas Andrusch, Jeanette Klenner, Piotr Wojciech Dabrowski, Martin S. Lindner, Andreas Nitsche, Bernhard Y. Renard

Source: Life, Vol 12, Iss 9, p 1345 (2022)

Subject Terms: NGS, metagenomics, viruses, infectious diseases, diagnostics, live sequencing, Science

File Description: electronic resource

Relation: https://www.mdpi.com/2075-1729/12/9/1345; https://doaj.org/toc/2075-1729

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Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany

Authors: Laura Uelze, Natalie Becker, Maria Borowiak, Ulrich Busch, Alexandra Dangel, Carlus Deneke, Jennie Fischer, Antje Flieger, Sabrina Hepner, Ingrid Huber, Ulrich Methner, Jörg Linde, Michael Pietsch, Sandra Simon, Andreas Sing, Simon H. Tausch, Istvan Szabo, Burkhard Malorny

Source: Frontiers in Microbiology, Vol 12 (2021)

Subject Terms: Salmonella, surveillance, food-borne disease outbreak, whole genome sequencing, cgMLST, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.626941/full; https://doaj.org/toc/1664-302X

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Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset

Authors: Dirk Höper, Josephine Grützke, Annika Brinkmann, Joël Mossong, Sébastien Matamoros, Richard J. Ellis, Carlus Deneke, Simon H. Tausch, Isabel Cuesta, Sara Monzón, Miguel Juliá, Thomas Nordahl Petersen, Rene S. Hendriksen, Sünje J. Pamp, Mikael Leijon, Mikhayil Hakhverdyan, Aaron M. Walsh, Paul D. Cotter, Lakshmi Chandrasekaran, Moon Y. F. Tay, Joergen Schlundt, Claudia Sala, Alessandra De Cesare, Andreas Nitsche, Martin Beer, Claudia Wylezich

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: background contamination, diagnostic assessment, high-throughput sequencing, metagenomics, pathogen, proficiency test, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2020.575377/full; https://doaj.org/toc/1664-302X

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German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing

Authors: Laura Uelze, Maria Borowiak, Markus Bönn, Erik Brinks, Carlus Deneke, Thomas Hankeln, Sylvia Kleta, Larissa Murr, Kerstin Stingl, Kathrin Szabo, Simon H. Tausch, Anne Wöhlke, Burkhard Malorny

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: interlaboratory study, whole-genome sequencing, food safety, illumina, ion torrent, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.573972/full; https://doaj.org/toc/1664-302X

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Whole Genome Sequence Analysis of a Prototype Strain of the Novel Putative Rotavirus Species L

Authors: Reimar Johne, Katja Schilling-Loeffler, Rainer G. Ulrich, Simon H. Tausch

Source: Viruses, Vol 14, Iss 3, p 462 (2022)

Subject Terms: rotavirus, genome sequence, taxonomy, phylogeny, virus species, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/14/3/462; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/3678e2d9af6d4f32a262b41005d62afe

Berlin Squirrelpox Virus, a New Poxvirus in Red Squirrels, Berlin, Germany

Authors: Gudrun Wibbelt, Simon H. Tausch, Piotr W. Dabrowski, Olivia Kershaw, Andreas Nitsche, Livia Schrick

Source: Emerging Infectious Diseases, Vol 23, Iss 10, Pp 1726-1729 (2017)

Subject Terms: squirrelpox, poxvirus, squirrel, Sciuridae, Berlin, Germany, Medicine, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://wwwnc.cdc.gov/eid/article/23/10/17-1008_article; https://doaj.org/toc/1080-6040; https://doaj.org/toc/1080-6059

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Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing

Authors: Josephine Grützke, Burkhard Malorny, Jens Andre Hammerl, Anne Busch, Simon H. Tausch, Herbert Tomaso, Carlus Deneke

Source: Frontiers in Microbiology, Vol 10 (2019)

Subject Terms: metagenomics, food safety, mock community, bioinformatics, shotgun, 16S, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2019.01805/full; https://doaj.org/toc/1664-302X

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What WGS Reveals about Salmonella enterica subsp. enterica in Wildlife in Germany

Authors: Laura Uelze, Angelina Bloch, Maria Borowiak, Mirjam Grobbel, Carlus Deneke, Matthias Fischer, Burkhard Malorny, Michael Pietsch, Sandra Simon, István Szabó, Simon H. Tausch, Jennie Fischer

Source: Microorganisms, Vol 9, Iss 9, p 1911 (2021)

Subject Terms: Salmonella enterica subsp. enterica, whole-genome sequencing, wildlife, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/9/9/1911; https://doaj.org/toc/2076-2607

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Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli

Authors: Katharina Juraschek, Maria Borowiak, Simon H. Tausch, Burkhard Malorny, Annemarie Käsbohrer, Saria Otani, Stefan Schwarz, Diana Meemken, Carlus Deneke, Jens Andre Hammerl

Source: Microorganisms, Vol 9, Iss 3, p 598 (2021)

Subject Terms: AMR, mobile genetic elements, qnrS, hybrid assembly, long-read sequencing, short-read sequencing, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/9/3/598; https://doaj.org/toc/2076-2607

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First Detection of GES-5-Producing Escherichia coli from Livestock—An Increasing Diversity of Carbapenemases Recognized from German Pig Production

Authors: Alexandra Irrgang, Simon H. Tausch, Natalie Pauly, Mirjam Grobbel, Annemarie Kaesbohrer, Jens A. Hammerl

Source: Microorganisms, Vol 8, Iss 10, p 1593 (2020)

Subject Terms: carbapenemase, CPE, GES-5, GES-5B, whole-genome sequencing, livestock, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/8/10/1593; https://doaj.org/toc/2076-2607

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Establishment of a Plasmid-Based Reverse Genetics System for the Cell Culture-Adapted Hepatitis E Virus Genotype 3c Strain 47832c

Authors: Johannes Scholz, Christine Bächlein, Ashish K. Gadicherla, Alexander Falkenhagen, Simon H. Tausch, Reimar Johne

Source: Pathogens, Vol 9, Iss 3, p 157 (2020)

Subject Terms: hepatitis e virus, genotype 3c, cell culture, reverse genetics system, site-directed mutagenesis, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-0817/9/3/157; https://doaj.org/toc/2076-0817

Access URL: https://doaj.org/article/9c98df9ad7d94e5aa7f3f87c80cbc11e

Whole Genome Characterization of Orthopoxvirus (OPV) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses

Authors: Cesare E. M. Gruber, Emanuela Giombini, Marina Selleri, Simon H. Tausch, Andreas Andrusch, Alona Tyshaieva, Giusy Cardeti, Raniero Lorenzetti, Lorenzo De Marco, Fabrizio Carletti, Andreas Nitsche, Maria R. Capobianchi, Giuseppe Ippolito, Gian Luca Autorino, Concetta Castilletti

Source: Viruses, Vol 10, Iss 10, p 546 (2018)

Subject Terms: OPV Abatino, orthopoxvirus, cowpox virus, ectromelia virus, phylogenetic tree, core gene set, Microbiology, QR1-502

File Description: electronic resource

Relation: http://www.mdpi.com/1999-4915/10/10/546; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/929289ac68974219b598c5a0891956d9

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

Authors: Simon H Tausch, Bernhard Y Renard, Andreas Nitsche, Piotr Wojciech Dabrowski

Source: PLoS ONE, Vol 10, Iss 9, p e0137896 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4574938?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/22385c9c37834927938a35b2fcac801c