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Diaz-Cánova D, Moens U, Brinkmann A, Nitsche A, Okeke MI. Whole genome sequencing of recombinant viruses obtained from co-infection and superinfection of Vero cells with modified vaccinia virus ankara vectored influenza vaccine and a naturally occurring cowpox virus. Front Immunol 2024; 15:1277447. [PMID: 38633245 PMCID: PMC11021749 DOI: 10.3389/fimmu.2024.1277447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Modified vaccinia virus Ankara (MVA) has been widely tested in clinical trials as recombinant vector vaccine against infectious diseases and cancers in humans and animals. However, one biosafety concern about the use of MVA vectored vaccine is the potential for MVA to recombine with naturally occurring orthopoxviruses in cells and hosts in which it multiplies poorly and, therefore, producing viruses with mosaic genomes with altered genetic and phenotypic properties. We previously conducted co-infection and superinfection experiments with MVA vectored influenza vaccine (MVA-HANP) and a feline Cowpox virus (CPXV-No-F1) in Vero cells (that were semi-permissive to MVA infection) and showed that recombination occurred in both co-infected and superinfected cells. In this study, we selected the putative recombinant viruses and performed genomic characterization of these viruses. Some putative recombinant viruses displayed plaque morphology distinct of that of the parental viruses. Our analysis demonstrated that they had mosaic genomes of different lengths. The recombinant viruses, with a genome more similar to MVA-HANP (>50%), rescued deleted and/or fragmented genes in MVA and gained new host ranges genes. Our analysis also revealed that some MVA-HANP contained a partially deleted transgene expression cassette and one recombinant virus contained part of the transgene expression cassette similar to that incomplete MVA-HANP. The recombination in co-infected and superinfected Vero cells resulted in recombinant viruses with unpredictable biological and genetic properties as well as recovery of delete/fragmented genes in MVA and transfer of the transgene into replication competent CPXV. These results are relevant to hazard characterization and risk assessment of MVA vectored biologicals.
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Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Malachy Ifeanyi Okeke
- Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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Brinkmann A, Pape K, Uddin S, Woelk N, Förster S, Jessen H, Michel J, Kohl C, Schaade L, Nitsche A. Genome sequencing of the mpox virus 2022 outbreak with amplicon-based Oxford Nanopore MinION sequencing. J Virol Methods 2024; 325:114888. [PMID: 38246565 DOI: 10.1016/j.jviromet.2024.114888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
We present an amplicon-based assay for MinION Nanopore sequencing of mpox virus (MPXV) genomes from clinical specimens, obtaining high-quality results with an average genome coverage of 99% for Ct values of up to 25, and a genome coverage of 97.1% for Ct values from 25 to 30 which are challenging to sequence. This assay is easy to implement in PCR-based workflows and provides accurate genomic data within a short time.
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany.
| | - Katharina Pape
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Niklas Woelk
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Heiko Jessen
- Praxis Jessen and Colleagues, Motzstraße 19, 10777 Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Claudia Kohl
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
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Souza ARV, Brinkmann A, Esparza J, Nitsche A, Damaso CR. Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines. mBio 2023; 14:e0188723. [PMID: 37729584 PMCID: PMC10653919 DOI: 10.1128/mbio.01887-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Modern smallpox vaccines, such as those used against mpox, are made from vaccinia viruses, but it is still unknown whether cowpox, horsepox, or vaccinia viruses were used in the early 20th century or earlier. The mystery began to be solved when the genomes of six historical smallpox vaccines used in the United States from 1850 to 1902 were determined. Our work analyzed in detail the genomes of these six historical vaccines, revealing a complex genomic structure. Historical vaccines are highly similar to horsepox in the core of their genomes, but some are closer to the structure of vaccinia virus at the ends of the genome. One of the vaccines is a recombinant virus with parts of variola virus recombined into its genome. Our data add valuable information for understanding the evolutionary path of current smallpox vaccines and the genetic makeup of the potentially extinct group of horsepox viruses.
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Affiliation(s)
- Aline R. V. Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens 1 – Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - José Esparza
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens 1 – Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Clarissa R. Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Brinkmann A, Kohl C, Pape K, Bourquain D, Thürmer A, Michel J, Schaade L, Nitsche A. Extensive ITR expansion of the 2022 Mpox virus genome through gene duplication and gene loss. Virus Genes 2023:10.1007/s11262-023-02002-1. [PMID: 37256469 DOI: 10.1007/s11262-023-02002-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023]
Abstract
Poxviruses are known to evolve slower than RNA viruses with only 1-2 mutations/genome/year. Rather than single mutations, rearrangements such as gene gain and loss, which have been discussed as a possible driver for host adaption, were described in poxviruses. In 2022 and 2023 the world is being challenged by the largest global outbreak so far of Mpox virus, and the virus seems to have established itself in the human community for an extended period of time. Here, we report five Mpox virus genomes from Germany with extensive gene duplication and loss, leading to the expansion of the ITR regions from 6400 to up to 24,600 bp. We describe duplications of up to 18,200 bp to the opposed genome end, and deletions at the site of insertion of up to 16,900 bp. Deletions and duplications of genes with functions of supposed immune modulation, virulence and host adaption as B19R, B21R, B22R and D10L are described. In summary, we highlight the need for monitoring rearrangements of the Mpox virus genome rather than for monitoring single mutations only.
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Affiliation(s)
- Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Katharina Pape
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology, Methodology and Research Infrastructure, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
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Nasri F, Kongkitimanon K, Wittig A, Cortés JS, Brinkmann A, Nitsche A, Schmachtenberg AJ, Renard BY, Fuchs S. MpoxRadar: a worldwide MPXV genomic surveillance dashboard. Nucleic Acids Res 2023:7160218. [PMID: 37167010 DOI: 10.1093/nar/gkad325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
The mpox virus (MPXV) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all MPXV genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them to the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of MPXV, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net.
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Affiliation(s)
- Ferdous Nasri
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Kunaphas Kongkitimanon
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Alice Wittig
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
- Genome Competence Center (MF1), Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Jorge Sánchez Cortés
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, Berlin 13353, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, Berlin 13353, Germany
| | - Anna-Juliane Schmachtenberg
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Stephan Fuchs
- Genome Competence Center (MF1), Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
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6
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM, Gibb K, Coventry K, Collignon P, Cassar S, Allerberger F, Begum A, Hossain ZZ, Worrell C, Vandenberg O, Pieters I, Victorien DT, Gutierrez ADS, Soria F, Grujić VR, Mazalica N, Rahube TO, Tagliati CA, Rodrigues D, Oliveira G, de Souza LCR, Ivanov I, Juste BI, Oumar T, Sopheak T, Vuthy Y, Ngandjio A, Nzouankeu A, Olivier ZAAJ, Yost CK, Kumar P, Brar SK, Tabo DA, Adell AD, Paredes-Osses E, Martinez MC, Cuadros-Orellana S, Ke C, Zheng H, Baisheng L, Lau LT, Chung T, Jiao X, Yu Y, JiaYong Z, Morales JFB, Valencia MF, Donado-Godoy P, Coulibaly KJ, Hrenovic J, Jergović M, Karpíšková R, Deogratias ZN, Elsborg B, Hansen LT, Jensen PE, Abouelnaga M, Salem MF, Koolmeister M, Legesse M, Eguale T, Heikinheimo A, Le Guyader S, Schaeffer J, Villacis JE, Sanneh B, Malania L, Nitsche A, Brinkmann A, Schubert S, Hesse S, Berendonk TU, Saba CKS, Mohammed J, Feglo PK, Banu RA, Kotzamanidis C, Lytras E, Lickes SA, Kocsis B, Solymosi N, Thorsteinsdottir TR, Hatha AM, Ballal M, Bangera SR, Fani F, Alebouyeh M, Morris D, O’Connor L, Cormican M, Moran-Gilad J, Battisti A, Diaconu EL, Corno G, Di Cesare A, Alba P, Hisatsune J, Yu L, Kuroda M, Sugai M, Kayama S, Shakenova Z, Kiiyukia C, Ng’eno E, Raka L, Jamil K, Fakhraldeen SA, Alaati T, Bērziņš A, Avsejenko J, Kokina K, Streikisa M, Bartkevics V, Matar GM, Daoud Z, Pereckienė A, Butrimaite-Ambrozeviciene C, Penny C, Bastaraud A, Rasolofoarison T, Collard JM, Samison LH, Andrianarivelo MR, Banda DL, Amin A, Rajandas H, Parimannan S, Spiteri D, Haber MV, Santchurn SJ, Vujacic A, Djurovic D, Bouchrif B, Karraouan B, Vubil DC, Pal P, Schmitt H, van Passel M, Jeunen GJ, Gemmell N, Chambers ST, Mendoza FP, Huete-Pιrez J, Vilchez S, Ahmed AO, Adisa IR, Odetokun IA, Fashae K, Sørgaard AM, Wester AL, Ryrfors P, Holmstad R, Mohsin M, Hasan R, Shakoor S, Gustafson NW, Schill CH, Rojas MLZ, Velasquez JE, Magtibay BB, Catangcatang K, Sibulo R, Yauce FC, Wasyl D, Manaia C, Rocha J, Martins J, Álvaro P, Di Yoong Wen D, Shin H, Hur HG, Yoon S, Bosevska G, Kochubovski M, Cojocaru R, Burduniuc O, Hong PY, Perry MR, Gassama A, Radosavljevic V, Tay MYF, Zuniga-Montanez R, Wuertz S, Gavačová D, Pastuchová K, Truska P, Trkov M, Keddy K, Esterhuyse K, Song MJ, Quintela-Baluja M, Lopez MG, Cerdà-Cuéllar M, Perera RRDP, Bandara NKBKRGW, Premasiri HI, Pathirage S, Charlemagne K, Rutgersson C, Norrgren L, Örn S, Boss R, Van der Heijden T, Hong YP, Kumburu HH, Mdegela RH, Hounmanou YMG, Chonsin K, Suthienkul O, Thamlikitkul V, de Roda Husman AM, Bidjada B, Njanpop-Lafourcade BM, Nikiema-Pessinaba SC, Levent B, Kurekci C, Ejobi F, Kalule JB, Thomsen J, Obaidi O, Jassim LM, Moore A, Leonard A, Graham DW, Bunce JT, Zhang L, Gaze WH, Lefor B, Capone D, Sozzi E, Brown J, Meschke JS, Sobsey MD, Davis M, Beck NK, Sukapanpatharam P, Truong P, Lilienthal R, Kang S, Wittum TE, Rigamonti N, Baklayan P, Van CD, Tran DMN, Do Phuc N, Kwenda G, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2023; 14:178. [PMID: 36635285 PMCID: PMC9837105 DOI: 10.1038/s41467-023-35890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick Munk
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christian Brinch
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N. Petersen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S. Hendriksen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S. Kjeldgaard
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M. Aarestrup
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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Stoliaroff-Pepin A, Peine C, Herath T, Lachmann J, Perriat D, Dörre A, Nitsche A, Michel J, Grossegesse M, Hofmann N, Rinner T, Kohl C, Brinkmann A, Meyer T, Dorner BG, Stern D, Treindl F, Hein S, Werel L, Hildt E, Gläser S, Schühlen H, Isner C, Peric A, Ghouzi A, Reichardt A, Janneck M, Lock G, Schaade L, Wichmann O, Harder T. Effectiveness of vaccines in preventing hospitalization due to COVID-19: A multicenter hospital-based case-control study, Germany, June 2021 to January 2022. Vaccine 2023; 41:290-293. [PMID: 36509640 PMCID: PMC9715487 DOI: 10.1016/j.vaccine.2022.11.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
We included 852 patients in a prospectively recruiting multicenter matched case-control study in Germany to assess vaccine effectiveness (VE) in preventing COVID-19-associated hospitalization during the Delta-variant dominance. The two-dose VE was 89 % (95 % CI 84-93 %) overall, 79 % in patients with more than two comorbidities and 77 % in adults aged 60-75 years. A third dose increased the VE to more than 93 % in all patient-subgroups.
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Affiliation(s)
- Anna Stoliaroff-Pepin
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany.
| | - Caroline Peine
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany.
| | - Tim Herath
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany
| | - Johannes Lachmann
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany
| | - Delphine Perriat
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany
| | - Achim Dörre
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Marica Grossegesse
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Natalie Hofmann
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Germany
| | - Tanja Meyer
- Centre for Biological Threats and Special Pathogens, ZBS3 Biological Toxins, Robert Koch Institute, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens, ZBS3 Biological Toxins, Robert Koch Institute, Germany
| | - Daniel Stern
- Centre for Biological Threats and Special Pathogens, ZBS3 Biological Toxins, Robert Koch Institute, Germany
| | - Fridolin Treindl
- Centre for Biological Threats and Special Pathogens, ZBS3 Biological Toxins, Robert Koch Institute, Germany
| | - Sascha Hein
- Division Virology, Paul-Ehrlich-Institute, Germany
| | - Laura Werel
- Division Virology, Paul-Ehrlich-Institute, Germany
| | | | - Sven Gläser
- Klinik für Innere Medizin - Pneumologie und Infektiologie, Vivantes Klinikum Neukölln und Spandau, Berlin, Germany
| | - Helmut Schühlen
- Vivantes Netzwerk für Gesundheit GmbH, Direktorat Klinische Forschung & Akademische Lehre, Berlin, Germany
| | - Caroline Isner
- Klinik für Innere Medizin - Infektiologie, Vivantes Auguste-Viktoria-Klinikum, Rubensstr. 125, 12157 Berlin, Germany
| | - Alexander Peric
- Klinik für Pneumologie und Infektiologie, Vivantes Klinikum im Friedrichshain, Landsberger Allee 49, 10249 Berlin, Germany
| | - Ammar Ghouzi
- Schön Klinik Düsseldorf, Interdisziplinäre Notaufnahme, Am Heerdter Krankenhaus 2, 40549 Düsseldorf, Germany
| | - Annette Reichardt
- Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125 Berlin, Germany
| | - Matthias Janneck
- Klinik für Kardiologie, Sektion Nephrologie, Albertinen Krankenhaus, Süntelstraße 11a, 22457 Hamburg, Germany
| | - Guntram Lock
- Klinik für Innere Medizin, Albertinen Krankenhaus, Süntelstraße 11a, 22457 Hamburg, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Germany
| | - Ole Wichmann
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany
| | - Thomas Harder
- Department for Infectious Disease Epidemiology, Immunization Unit, Robert Koch Institute, Germany
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Calderón JPR, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, von Kleist M, Kröger S, Wolff T. 1358. Establishing Genomic SARS-CoV-2 Surveillance at the National Level: Germany, 2021. Open Forum Infect Dis 2022. [PMCID: PMC9752442 DOI: 10.1093/ofid/ofac492.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance. Methods SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences. Results We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. Conclusion This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
- Djin-Ye Oh
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | - Martin Hölzer
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | - Matthias Budt
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | - Janine Reiche
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | | | - Sascha Hein
- Paul Ehrlich Institute, Berlin, Berlin, Germany
| | | | - Walter Haas
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | - Ralf Dürrwald
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Berlin, Germany
| | - Stephan Fuchs
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Stefan Kröger
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
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9
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Michel J, Targosz A, Rinner T, Bourquain D, Brinkmann A, Sacks JA, Schaade L, Nitsche A. Evaluation of 11 commercially available PCR kits for the detection of monkeypox virus DNA, Berlin, July to September 2022. Euro Surveill 2022; 27:2200816. [PMID: 36367010 PMCID: PMC9650706 DOI: 10.2807/1560-7917.es.2022.27.45.2200816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Before the international spread of monkeypox in May 2022, PCR kits for the detection of orthopoxviruses, and specifically monkeypox virus, were rarely available. Here we describe the evaluation of 11 recently developed commercially available PCR kits for the detection of monkeypox virus DNA. All tested kits are currently intended for research use only and clinical performance still needs to be assessed in more detail, but all were suitable for diagnostics of monkeypox virus, with variations in specificity rather than sensitivity.
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Affiliation(s)
- Janine Michel
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Angelina Targosz
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Thomas Rinner
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Daniel Bourquain
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Annika Brinkmann
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Jilian Amber Sacks
- World Health Organization (WHO), Department of Epidemic and Pandemic Preparedness and Prevention, Geneva, Switzerland
| | - Lars Schaade
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
| | - Andreas Nitsche
- Robert Koch Institute (RKI), Center for Biological Threats and Special Pathogens, German Reference Laboratory for Poxviruses, Berlin, Germany
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10
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Ramos Calderón JP, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, Kröger S, von Kleist M, Wolff T. Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021. Clin Infect Dis 2022; 75:S110-S120. [PMID: 35749674 PMCID: PMC9278222 DOI: 10.1093/cid/ciac399] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany. METHODS At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. RESULTS We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. CONCLUSIONS SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.
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Affiliation(s)
- Djin Ye Oh
- Correspondence: D.-Y. Oh Robert Koch Institute, Dept. of Infectious Diseases, Seestr. 10, 13353 Berlin, Germany ()
| | | | - Sofia Paraskevopoulou
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Maria Trofimova
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
| | - Felix Hartkopf
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Matthias Budt
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Marianne Wedde
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Berit Haldemann
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Janine Reiche
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Kathrin Keeren
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Aleksandar Radonić
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | | | | | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS1), Robert Koch Institute, Berlin, Germany
| | - Kathrin Trappe
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Oliver Drechsel
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Kathleen Klaper
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany,Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch Institute, Berlin, Germany
| | - Sascha Hein
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Eberhardt Hildt
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Walter Haas
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms (P3), Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Andrea Thürmer
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
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11
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Diaz-Cánova D, Moens UL, Brinkmann A, Nitsche A, Okeke MI. Genomic Sequencing and Analysis of a Novel Human Cowpox Virus With Mosaic Sequences From North America and Old World Orthopoxvirus. Front Microbiol 2022; 13:868887. [PMID: 35592007 PMCID: PMC9112427 DOI: 10.3389/fmicb.2022.868887] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Orthopoxviruses (OPXVs) not only infect their natural hosts, but some OPXVs can also cause disease in humans. Previously, we partially characterized an OPXV isolated from an 18-year-old male living in Northern Norway. Restriction enzyme analysis and partial genome sequencing characterized this virus as an atypical cowpox virus (CPXV), which we named CPXV-No-H2. In this study, we determined the complete genome sequence of CPXV-No-H2 using Illumina and Nanopore sequencing. Our results showed that the whole CPXV-No-H2 genome is 220,276 base pairs (bp) in length, with inverted terminal repeat regions of approximately 7 kbp, containing 217 predicted genes. Seventeen predicted CPXV-No-H2 proteins were most similar to OPXV proteins from the Old World, including Ectromelia virus (ECTV) and Vaccinia virus, and North America, Alaskapox virus (AKPV). CPXV-No-H2 has a mosaic genome with genes most similar to other OPXV genes, and seven potential recombination events were identified. The phylogenetic analysis showed that CPXV-No-H2 formed a separate clade with the German CPXV isolates CPXV_GerMygEK938_17 and CPXV_Ger2010_MKY, sharing 96.4 and 96.3% nucleotide identity, respectively, and this clade clustered closely with the ECTV-OPXV Abatino clade. CPXV-No-H2 is a mosaic virus that may have arisen out of several recombination events between OPXVs, and its phylogenetic clustering suggests that ECTV-Abatino-like cowpox viruses form a distinct, new clade of cowpox viruses.
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Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo L Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Malachy Ifeanyi Okeke
- Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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12
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Brinkmann A, Uddin S, Ulm SL, Pape K, Förster S, Enan K, Nourlil J, Krause E, Schaade L, Michel J, Nitsche A. RespiCoV: Simultaneous identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and 46 respiratory tract viruses and bacteria by amplicon-based Oxford-Nanopore MinION sequencing. PLoS One 2022; 17:e0264855. [PMID: 35263362 PMCID: PMC8906600 DOI: 10.1371/journal.pone.0264855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/17/2022] [Indexed: 11/18/2022] Open
Abstract
Since December 2019 the world has been facing the outbreak of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Identification of infected patients and discrimination from other respiratory infections have so far been accomplished by using highly specific real-time PCRs. Here we present a rapid multiplex approach (RespiCoV), combining highly multiplexed PCRs and MinION sequencing suitable for the simultaneous screening for 41 viral and five bacterial agents related to respiratory tract infections, including the human coronaviruses NL63, HKU1, OC43, 229E, Middle East respiratory syndrome coronavirus, SARS-CoV, and SARS-CoV-2. RespiCoV was applied to 150 patient samples with suspected SARS-CoV-2 infection and compared with specific real-time PCR. Additionally, several respiratory tract pathogens were identified in samples tested positive or negative for SARS-CoV-2. Finally, RespiCoV was experimentally compared to the commercial RespiFinder 2SMART multiplex screening assay (PathoFinder, The Netherlands).
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
- * E-mail:
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie-Luisa Ulm
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Katharina Pape
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Khalid Enan
- Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | | | - Eva Krause
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
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13
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Brinkmann A, Ulm SL, Uddin S, Förster S, Seifert D, Oehme R, Corty M, Schaade L, Michel J, Nitsche A. AmpliCoV: Rapid Whole-Genome Sequencing Using Multiplex PCR Amplification and Real-Time Oxford Nanopore MinION Sequencing Enables Rapid Variant Identification of SARS-CoV-2. Front Microbiol 2021; 12:651151. [PMID: 34276587 PMCID: PMC8281033 DOI: 10.3389/fmicb.2021.651151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/01/2021] [Indexed: 11/22/2022] Open
Abstract
Since the emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in December 2019, the scientific community has been sharing data on epidemiology, diagnostic methods, and whole-genomic sequences almost in real time. The latter have already facilitated phylogenetic analyses, transmission chain tracking, protein modeling, the identification of possible therapeutic targets, timely risk assessment, and identification of novel variants. We have established and evaluated an amplification-based approach for whole-genome sequencing of SARS-CoV-2. It can be used on the miniature-sized and field-deployable sequencing device Oxford Nanopore MinION, with sequencing library preparation time of 10 min. We show that the generation of 50,000 total reads per sample is sufficient for a near complete coverage (>90%) of the SARS-CoV-2 genome directly from patient samples even if virus concentration is low (Ct 35, corresponding to approximately 5 genome copies per reaction). For patient samples with high viral load (Ct 18–24), generation of 50,000 reads in 1–2 h was shown to be sufficient for a genome coverage of >90%. Comparison to Illumina data reveals an accuracy that suffices to identify virus mutants. AmpliCoV can be applied whenever sequence information on SARS-CoV-2 is required rapidly, for instance for the identification of circulating virus mutants.
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie-Luisa Ulm
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Dominique Seifert
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Rainer Oehme
- Landesgesundheitsamt Baden-Württemberg, Stuttgart, Germany
| | - Merle Corty
- LADR Laboratory Group Dr. Kramer & Colleagues, Geesthacht, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
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14
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Michel J, Neumann M, Krause E, Rinner T, Muzeniek T, Grossegesse M, Hille G, Schwarz F, Puyskens A, Förster S, Biere B, Bourquain D, Domingo C, Brinkmann A, Schaade L, Schrick L, Nitsche A. Resource-efficient internally controlled in-house real-time PCR detection of SARS-CoV-2. Virol J 2021; 18:110. [PMID: 34078394 PMCID: PMC8170437 DOI: 10.1186/s12985-021-01559-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
Background The reliable detection of SARS-CoV-2 has become one of the most important contributions to COVID-19 crisis management. With the publication of the first sequences of SARS-CoV-2, several diagnostic PCR assays have been developed and published. In addition to in-house assays the market was flooded with numerous commercially available ready-to-use PCR kits, with both approaches showing alarming shortages in reagent supply. Aim Here we present a resource-efficient in-house protocol for the PCR detection of SARS-CoV-2 RNA in patient specimens (RKI/ZBS1 SARS-CoV-2 protocol). Methods Two duplex one-step real-time RT-PCR assays are run simultaneously and provide information on two different SARS-CoV-2 genomic regions. Each one is duplexed with a control that either indicates potential PCR inhibition or proves the successful extraction of nucleic acid from the clinical specimen. Results Limit of RNA detection for both SARS-CoV-2 assays is below 10 genomes per reaction. The protocol enables testing specimens in duplicate across the two different SARS-CoV-2 PCR assays, saving reagents by increasing testing capacity. The protocol can be run on various PCR cyclers with several PCR master mix kits. Conclusion The presented RKI/ZBS1 SARS-CoV-2 protocol represents a cost-effective alternative in times of shortages when commercially available ready-to-use kits may not be available or affordable. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01559-3.
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Affiliation(s)
- Janine Michel
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Markus Neumann
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Eva Krause
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Therese Muzeniek
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Marica Grossegesse
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Georg Hille
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Franziska Schwarz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Puyskens
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Sophie Förster
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Barbara Biere
- Influenza and Other Respiratory Viruses (FG 17), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Cristina Domingo
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Livia Schrick
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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15
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Appelt S, Rohleder AM, Invernizzi C, Mikulak R, Brinkmann A, Nitsche A, Krüger M, Dorner MB, Dorner BG, Scholz HC, Grunow R. Strengthening the United Nations Secretary-General's Mechanism to an alleged use of bioweapons through a quality-assured laboratory response. Nat Commun 2021; 12:3078. [PMID: 34035242 PMCID: PMC8149868 DOI: 10.1038/s41467-021-23296-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/23/2021] [Indexed: 12/01/2022] Open
Abstract
The cascade of innovations in biotechnology opens new pathways for biological warfare. The international laboratory network being developed under the UN Secretary-General’s Mechanism could provide vital evidence in case of an alleged biological attack.
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Affiliation(s)
- Sandra Appelt
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Anna-Maria Rohleder
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | | | - Robert Mikulak
- Biological Policy Staff, Bureau of International Security and Nonproliferation, U.S. Department of State, Washington, USA
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Maren Krüger
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Martin B Dorner
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany
| | - Holger C Scholz
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany.
| | - Roland Grunow
- Centre for Biological Threats and Special Pathogens (ZBS 1, ZBS 2 and ZBS 3), Robert Koch Institute, Berlin, Germany.
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16
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Brinkmann A, Souza ARV, Esparza J, Nitsche A, Damaso CR. Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA. Genome Biol 2020; 21:286. [PMID: 33272280 PMCID: PMC7716468 DOI: 10.1186/s13059-020-02202-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/11/2020] [Indexed: 11/10/2022] Open
Abstract
According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the different smallpox vaccine genomes during the centuries. We re-assembled the genomes, which include the largest genomes in the vaccinia lineage and one true horsepox strain. Moreover, the assemblies reveal a diverse genetic structure in the genome ends. Our data emphasize the concurrent use of horsepox and horsepox-related viruses as the smallpox vaccine in the nineteenth century.
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Affiliation(s)
- Annika Brinkmann
- Centre for Biological Threats and Special Pathogens 1 - Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Aline R V Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - CCS, Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - José Esparza
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens 1 - Highly Pathogenic Viruses & German Consultant Laboratory for Poxviruses & WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Clarissa R Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - CCS, Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil.
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17
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Sala C, Mordhorst H, Grützke J, Brinkmann A, Petersen TN, Poulsen C, Cotter PD, Crispie F, Ellis RJ, Castellani G, Amid C, Hakhverdyan M, Guyader SL, Manfreda G, Mossong J, Nitsche A, Ragimbeau C, Schaeffer J, Schlundt J, Tay MYF, Aarestrup FM, Hendriksen RS, Pamp SJ, De Cesare A. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms 2020; 8:microorganisms8121861. [PMID: 33255715 PMCID: PMC7760972 DOI: 10.3390/microorganisms8121861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.
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Affiliation(s)
- Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40127 Bologna, Italy;
| | - Hanne Mordhorst
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Josephine Grützke
- German Federal Institute for Risk Assessment, Department of Biological Safety, 12277 Berlin, Germany;
| | - Annika Brinkmann
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (A.B.); (A.N.)
| | - Thomas N. Petersen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Casper Poulsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and Vistamilk, T12 YN60 Co. Cork, Ireland; (P.D.C.); (F.C.)
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and Vistamilk, T12 YN60 Co. Cork, Ireland; (P.D.C.); (F.C.)
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, APHA Weybridge, Addlestone, Surrey, KT15 3NB, UK;
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40127 Bologna, Italy;
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
| | | | - Soizick Le Guyader
- Laboratoire de Microbiologie, CEDEX 03, 44311 Nantes, France; (S.L.G.); (J.S.)
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy;
| | - Joël Mossong
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg; (J.M.); (C.R.)
| | - Andreas Nitsche
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (A.B.); (A.N.)
| | - Catherine Ragimbeau
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg; (J.M.); (C.R.)
| | - Julien Schaeffer
- Laboratoire de Microbiologie, CEDEX 03, 44311 Nantes, France; (S.L.G.); (J.S.)
| | - Joergen Schlundt
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), 62 Nanyang Dr, Singapore 637459, Singapore; (J.S.); (M.Y.F.T.)
| | - Moon Y. F. Tay
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), 62 Nanyang Dr, Singapore 637459, Singapore; (J.S.); (M.Y.F.T.)
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Rene S. Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kgs, 2800 Lyngby, Denmark; (H.M.); (T.N.P.); (C.P.); (F.M.A.); (R.S.H.); (S.J.P.)
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell’Emilia, Italy
- Correspondence:
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18
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Richter DC, Brenner T, Brinkmann A, Grabein B, Hochreiter M, Heininger A, Störzinger D, Briegel J, Pletz M, Weigand MA, Lichtenstern C. [New antibiotics for severe infections due to multidrug-resistant pathogens : Definitive treatment and escalation]. Anaesthesist 2020; 68:785-800. [PMID: 31555832 DOI: 10.1007/s00101-019-00646-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multidrug-resistant pathogens often lead to treatment failure of antimicrobial regimens. After a period of imbalance between the occurrence/spread of resistance mechanisms and the development of new substances, some new substances have meanwhile been approved and many more are currently undergoing clinical testing. They are particularly effective against specific resistance mechanisms/pathogens and should be preserved for definitive treatment of an isolated pathogen. In the absence of alternatives reserve antibiotics, such as aztreonam and colistin have experienced a renaissance. They are again used in special infection scenarios and clinically tested in combination with new substances. Despite the introduction and development of new substances the building of resistance will at some time also render these (at least partially) ineffective. Therefore, their implementation must be carried out according to the antibiotic or infectious diseases stewardship.
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Affiliation(s)
- D C Richter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland.
| | - T Brenner
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Heidenheim, Deutschland
| | - B Grabein
- Stabsstelle "Klinische Mikrobiologie und Krankenhaushygiene", Klinikum der Universität München, München, Deutschland
| | - M Hochreiter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - A Heininger
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - D Störzinger
- Apotheke, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - J Briegel
- Klinik für Anästhesiologie, Ludwig-Maximilians-Universität, München, Deutschland
| | - M Pletz
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - M A Weigand
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - C Lichtenstern
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
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19
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Höper D, Grützke J, Brinkmann A, Mossong J, Matamoros S, Ellis RJ, Deneke C, Tausch SH, Cuesta I, Monzón S, Juliá M, Petersen TN, Hendriksen RS, Pamp SJ, Leijon M, Hakhverdyan M, Walsh AM, Cotter PD, Chandrasekaran L, Tay MYF, Schlundt J, Sala C, De Cesare A, Nitsche A, Beer M, Wylezich C. Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset. Front Microbiol 2020; 11:575377. [PMID: 33250869 PMCID: PMC7672002 DOI: 10.3389/fmicb.2020.575377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/13/2020] [Indexed: 01/16/2023] Open
Abstract
Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants' reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary.
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Affiliation(s)
- Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Joël Mossong
- Département de Microbiologie, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Sébastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC University of Amsterdam, Amsterdam, Netherlands
| | | | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Miguel Juliá
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Thomas Nordahl Petersen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Rene S. Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Sünje J. Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Mikhayil Hakhverdyan
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Aaron M. Walsh
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Lakshmi Chandrasekaran
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Moon Y. F. Tay
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Joergen Schlundt
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Ergünay K, Dinçer E, Kar S, Emanet N, Yalçınkaya D, Polat Dinçer PF, Brinkmann A, Hacıoğlu S, Nitsche A, Özkul A, Linton YM. Multiple orthonairoviruses including Crimean-Congo hemorrhagic fever virus, Tamdy virus and the novel Meram virus in Anatolia. Ticks Tick Borne Dis 2020; 11:101448. [PMID: 32723637 DOI: 10.1016/j.ttbdis.2020.101448] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 02/08/2023]
Abstract
We conducted orthonairovirus RNA screening of 7043 tick specimens-representing 16 species-collected from various regions of Anatolia. In 602 pools, Crimean-Congo hemorrhagic fever virus (CCHFV) Europe 1 and 2 lineages were detected in seven pools (1.1 %) comprising Hyalomma marginatum, Hyalomma scupense, Rhipicephalus bursa, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus ticks. In pools of Hyalomma aegyptium, we detected Tamdy virus (TAMV) and an unclassified nairovirus sequence. Next-generation sequencing revealed complete coding regions of three CCHFV Europe 2 (AP92-like) viruses, TAMV and the novel orthonairovirus, tentatively named herein as Meram virus. We further performed in silico functional analysis of all available CCHFV Europe 2, TAMV, Meram and related virus genomes. The CCHFV Europe 2 viruses possessed several conserved motifs, including those with OTU-like cysteine protease activity. Probable recombinations were identified in L genome segments of CCHFV and TAMV. Through phylogeny reconstruction using individual genome segments, Meram virus emerged as a distinct virus among species within the Orthonairovirus genus. It further exhibited conserved motifs associated with RNA binding, encapsidation, signal peptidase cleavage, post-translational modification, RNA-dependent RNA polymerase and OTU-like activities. Bole tick virus 3 was also detected in two pools with CCHFV reactivity. Hereby, we describe a novel tick-associated orthonairovirus, in a CCHFV-endemic region with confirmed TAMV activity. Human and animal health impact of these viruses need to be addressed.
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Affiliation(s)
- Koray Ergünay
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara 06100, Turkey.
| | - Ender Dinçer
- Dokuz Eylül University, Faculty of Veterinary Medicine, Department of Virology, İzmir 35890, Turkey
| | - Sırrı Kar
- Namık Kemal University, Department of Biology, Tekirdağ 33110, Turkey; University of Texas Medical Branch, Department of Microbiology and Immunology and Galveston National Laboratory, Galveston, GX 77555, USA
| | - Nergis Emanet
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara 06100, Turkey
| | | | - Pelin Fatoş Polat Dinçer
- Dokuz Eylül University, Faculty of Veterinary Medicine, Department of Internal Medicine, İzmir 35890, Turkey
| | - Annika Brinkmann
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin 13352, Germany
| | - Sabri Hacıoğlu
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, Ankara 06110, Turkey
| | - Andreas Nitsche
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin 13352, Germany
| | - Aykut Özkul
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, Ankara 06110, Turkey
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA; Department of Entomology, Smithsonian Institution - National Museum of Natural History, Washington, DC 20560, USA; Walter Reed Army Institute of Research (WRAIR), 503 Robert Grant Ave, Silver Spring, MD 20910, USA
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21
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Brinkmann A, Röhr AC, Frey OR, Krüger WA, Brenner T, Richter DC, Bodmann KF, Kresken M, Grabein B. [S2k guidelines of the PEG on calculated parenteral initial treatment of bacterial diseases in adults : Focussed summary and supplementary information on antibiotic treatment of critically ill patients]. Anaesthesist 2019; 67:936-949. [PMID: 30511110 DOI: 10.1007/s00101-018-0512-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In January 2018 the recent revision of the S2k guidelines on calculated parenteral initial treatment of bacterial diseases in adults-update 2018 (Editor: Paul Ehrlich Society for Chemotherapy, PEG) was realized. It is a helpful tool for the complex infectious disease setting in an intensive care unit. The present summary of the guidelines focuses on the topics of anti-infective agents, including new substances, pharmacokinetics and pharmacodynamics as well as on microbiology, resistance development and recommendations for calculated drug therapy in septic patients. As in past revisions the recent resistance situation and results of new clinical studies are considered and anti-infective agents are summarized in a table.
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Affiliation(s)
- A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustraße 100, 89522, Heidenheim, Deutschland.
| | - A C Röhr
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
| | - O R Frey
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
| | - W A Krüger
- Klinik für Anästhesiologie und Operative Intensivmedizin, Klinikum Konstanz, Konstanz, Deutschland
| | - T Brenner
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - D C Richter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - K-F Bodmann
- Klinik für Internistische Intensiv- und Notfallmedizin und Klinische Infektiologie, Klinikum Barnim GmbH, Werner Forßmann Krankenhaus, Eberswalde, Deutschland
| | - M Kresken
- Antiinfectives Intelligence GmbH, Campus Rheinbach, Hochschule Bonn-Rhein-Sieg, Rheinbach, Deutschland.,Rheinische Fachhochschule Köln gGmbH, Köln, Deutschland
| | - B Grabein
- Stabsstelle Klinische Mikrobiologie und Krankenhaushygiene, Klinikum der Universität München, Campus Großhadern, München, Deutschland
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22
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Dinçer E, Hacıoğlu S, Kar S, Emanet N, Brinkmann A, Nitsche A, Özkul A, Linton YM, Ergünay K. Survey and Characterization of Jingmen Tick Virus Variants. Viruses 2019; 11:v11111071. [PMID: 31744216 PMCID: PMC6893481 DOI: 10.3390/v11111071] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022] Open
Abstract
We obtained a Jingmen tick virus (JMTV) isolate, following inoculation of a tick pool with detectable Crimean-Congo hemorrhagic fever virus (CCHFV) RNA. We subsequently screened 7223 ticks, representing 15 species in five genera, collected from various regions in Anatolia and eastern Thrace, Turkey. Moreover, we tested specimens from various patient cohorts (n = 103), and canine (n = 60), bovine (n = 20) and avian specimens (n = 65). JMTV nucleic acids were detected in 3.9% of the tick pools, including those from several tick species from the genera Rhipicephalus and Haemaphysalis, and Hyalomma marginatum, the main vector of CCHFV in Turkey. Phylogenetic analysis supported two separate clades, independent of host or location, suggesting ubiquitous distribution in ticks. JMTV was not recovered from any human, animal or bird specimens tested. Near-complete viral genomes were sequenced from the prototype isolate and from three infected tick pools. Genome topology and functional organization were identical to the members of Jingmen group viruses. Phylogenetic reconstruction of individual viral genome segments and functional elements further supported the close relationship of the strains from Kosovo. We further identified probable recombination events in the JMTV genome, involving closely-related strains from Anatolia or China.
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Affiliation(s)
- Ender Dinçer
- Research and Application Center, Advanced Technology Education, Mersin University, Mersin 33110, Turkey;
| | - Sabri Hacıoğlu
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara 06110, Turkey; (S.H.)
| | - Sırrı Kar
- Department of Biology, Namık Kemal University, Tekirdağ 33110, Turkey;
- Department of Microbiology and Immunology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, GX 77555, USA
| | - Nergis Emanet
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey;
| | - Annika Brinkmann
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, 13352 Berlin, Germany; (A.B.); (A.N.)
| | - Andreas Nitsche
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, 13352 Berlin, Germany; (A.B.); (A.N.)
| | - Aykut Özkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara 06110, Turkey; (S.H.)
| | - Yvonne-Marie Linton
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, Washington, DC 20560, USA
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
| | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey;
- Correspondence: ; Tel.: +90-312-305-1560 (ext. 1465); Fax: 90-312-305-2161
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23
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Brinkmann A, Röhr AC, Köberer A, Fuchs T, Krüger WA, König C, Richter D, Weigand MA, Frey OR. [Adequate anti-infective treatment : Importance of individual dosing and application]. Anaesthesist 2019; 67:461-476. [PMID: 29766208 DOI: 10.1007/s00101-018-0443-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sepsis-induced changes in pharmacokinetic parameters are a well-known problem in intensive care medicine. Dosing of antibiotics in this setting is therefore challenging. Alterations to the substance-specific kinetics of anti-infective substances have an effect on the distribution and excretion processes in the body. Increased clearance and an increased distribution volume (Vd) and particularly compromized organ function with reduced antibiotic elimination are often encountered in patients with sepsis. Renal replacement treatment, which is frequently used in intensive care medicine, represents a substantial intervention in this system. Current international guidelines recommend individualized dosing strategies and adaptation of doses according to measured serum levels and pharmacokinetic/pharmacodynamic (PK/PD) parameters as concepts to optimize anti-infective therapy in the critically ill. Likewise, the recommendation to adjust the administration form of beta-lactam antibiotics to prolonged or continuous infusion can be found increasingly more often in the literature. This article reviews the background of the individual dosing in intensive care patients and their applicability to the clinical routine.
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Affiliation(s)
- A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustr. 100, 89522, Heidenheim, Deutschland.
| | - A C Röhr
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
| | - A Köberer
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustr. 100, 89522, Heidenheim, Deutschland
| | - T Fuchs
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustr. 100, 89522, Heidenheim, Deutschland
| | - W A Krüger
- Klinik für Anästhesiologie und Operative Intensivmedizin, Klinikum Konstanz, Konstanz, Deutschland
| | - C König
- Klinik für Intensivmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland.,Klinikapotheke, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - D Richter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - M A Weigand
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - O R Frey
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
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24
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Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets. J Clin Microbiol 2019; 57:e00466-19. [PMID: 31167846 PMCID: PMC6663916 DOI: 10.1128/jcm.00466-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Ariane Belka
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas Nordahl Petersen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Anna Papa
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Angeliki Melidou
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Erhard van der Vries
- Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
| | | | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Annelies Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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25
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Akıner MM, Öztürk M, Başer AB, Günay F, Hacıoğlu S, Brinkmann A, Emanet N, Alten B, Özkul A, Nitsche A, Linton YM, Ergünay K. Arboviral screening of invasive Aedes species in northeastern Turkey: West Nile virus circulation and detection of insect-only viruses. PLoS Negl Trop Dis 2019; 13:e0007334. [PMID: 31059502 PMCID: PMC6522068 DOI: 10.1371/journal.pntd.0007334] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/16/2019] [Accepted: 03/26/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The recent reports of Aedes aegypti and Ae. albopictus populations in Turkey, in parallel with the territorial expansion identified in several surrounding countries, have raised concerns about the establishment and re-establishment of these invasive Aedes mosquitoes in Turkey. This cross-sectional study was performed to detect Aedes aegypti and Ae. albopictus in regions of recent incursions, and screen for viral pathogens known to be transmitted elsewhere by these species. METHODOLOGY Mosquitoes were collected at several locations in Artvin, Rize and Trabzon provinces of the Black Sea region during 2016-2017, identified morphologically, pooled and analyzed via generic or specific nucleic acid amplification assays. Viruses in positive pools were identified by product sequencing, cell culture inoculation and next generation sequencing (NGS) in selected specimens. PRINCIPAL FINDINGS The study group comprised 791 specimens. Aedes albopictus was the most abundant species in all locations (89.6%), followed by Ae. aegypti (7.8%) and Culex pipiens (2.5%). Mosquitoes were screened for viruses in 65 pools where fifteen (23.1%) were reactive. The infecting strains was identified as West Nile virus (WNV) in 5 pools (7.7%) with Ae. albopictus or Cx. pipiens mosquitoes. The obtained WNV sequences phylogenetically grouped with local and global lineage 1 clade 1a viruses. In 4 (6.2%) and 6 (9.2%) pools, respectively, cell fusing agent virus (CFAV) and Aedes flavivirus (AEFV) sequences were characterized. NGS provided a near-complete AEFV genome in a pool of Ae. albopictus. The strain is provisionally called "AEFV-Turkey", and functional analysis of the genome revealed several conserved motifs and regions associated with virus replication. Merida-like virus Turkey (MERDLVT), a recently-described novel rhabdovirus, was also co-detected in a Cx. pipiens pool also positive for WNV. CONCLUSIONS/SIGNIFICANCE Invasive Aedes mosquitoes are established in certain locations of northeastern Turkey. Herein we conclusively show the role of these species in WNV circulation in the region. Biosurveillance is imperative to monitor the spread of these species further into Asia Minor and to detect possible introduction of pathogens.
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Affiliation(s)
- Mustafa M. Akıner
- Recep Tayyip Erdogan University, Faculty of Arts and Sciences, Department of Biology, Rize, TURKEY
| | - Murat Öztürk
- Recep Tayyip Erdogan University, Faculty of Arts and Sciences, Department of Biology, Rize, TURKEY
| | - Aykut Buğra Başer
- Recep Tayyip Erdogan University, Faculty of Arts and Sciences, Department of Biology, Rize, TURKEY
| | - Filiz Günay
- Hacettepe University; Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, TURKEY
| | - Sabri Hacıoğlu
- Ankara University; Faculty of Veterinary Medicine, Department of Virology, Ankara, TURKEY
| | - Annika Brinkmann
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, GERMANY
| | - Nergis Emanet
- Hacettepe University; Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, TURKEY
| | - Bülent Alten
- Hacettepe University; Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, TURKEY
| | - Aykut Özkul
- Ankara University; Faculty of Veterinary Medicine, Department of Virology, Ankara, TURKEY
| | - Andreas Nitsche
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, GERMANY
| | - Yvonne-Marie Linton
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, United States of America
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, United States of America
| | - Koray Ergünay
- Hacettepe University; Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, TURKEY
- * E-mail:
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Brinkmann A, Hekimoğlu O, Dincer E, Hagedorn P, Nitsche A, Ergünay K. A metagenomic survey of ticks reveals pathogenic rickettsia and francisella/coxiella-like endosymbionts in Anatolia. Int J Infect Dis 2019. [DOI: 10.1016/j.ijid.2018.11.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Brinkmann A, Hekimoğlu O, Dinçer E, Hagedorn P, Nitsche A, Ergünay K. A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia. Parasit Vectors 2019; 12:26. [PMID: 30635006 PMCID: PMC6329055 DOI: 10.1186/s13071-018-3277-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023] Open
Abstract
Background Ticks participate as arthropod vectors in the transmission of pathogenic microorganisms to humans. Several tick-borne infections have reemerged, along with newly described agents of unexplored pathogenicity. In an attempt to expand current information on tick-associated bacteria and protozoans, we performed a cross-sectional screening of ticks, using next-generation sequencing. Ticks seeking hosts and infesting domestic animals were collected in four provinces across the Aegean, Mediterranean and Central Anatolia regions of Turkey and analyzed by commonly used procedures and platforms. Results Two hundred and eighty ticks comprising 10 species were evaluated in 40 pools. Contigs from tick-associated microorganisms were detected in 22 (55%) questing and 4 feeding (10%) tick pools, with multiple microorganisms identified in 12 pools. Rickettsia 16S ribosomal RNA gene, gltA, sca1 and ompA sequences were present in 7 pools (17.5%), comprising feeding Haemaphysalis parva and questing/hunting Rhipicephalus bursa, Rhipicephalus sanguineus (sensu lato) and Hyalomma marginatum specimens. A near-complete genome and conjugative plasmid of a Rickettsia hoogstraalii strain could be characterized in questing Ha. parva. Coxiella-like endosymbionts were identified in pools of questing (12/40) as well as feeding (4/40) ticks of the genera Rhipicephalus, Haemaphysalis and Hyalomma. Francisella-like endosymbionts were also detected in 22.5% (9/40) of the pools that comprise hunting Hyalomma ticks in 8 pools. Coxiella-like and Francisella-like endosymbionts formed phylogenetically distinct clusters associated with their tick hosts. Borrelia turcica was characterized in 5% (2/40) of the pools, comprising hunting Hyalomma aegyptium ticks. Co-infection of Coxiella-like endosymbiont and Babesia was noted in a questing R. sanguineus (s.l.) specimen. Furthermore, protozoan 18S rRNA gene sequences were detected in 4 pools of questing/hunting ticks (10%) and identified as Babesia ovis, Hemolivia mauritanica, Babesia and Theileria spp. Conclusions Our metagenomic approach enabled identification of diverse pathogenic and non-pathogenic microorganisms in questing and feeding ticks in Anatolia. Electronic supplementary material The online version of this article (10.1186/s13071-018-3277-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annika Brinkmann
- Center for Biological Threats and Special Pathogens 1 (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Olcay Hekimoğlu
- Department of Biology, Division of Ecology, Hacettepe University, Faculty of Science, 06800, Ankara, Turkey
| | - Ender Dinçer
- Advanced Technology Education, Research and Application Center, Mersin University, 33110, Mersin, Turkey
| | - Peter Hagedorn
- Center for Biological Threats and Special Pathogens 1 (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Andreas Nitsche
- Center for Biological Threats and Special Pathogens 1 (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Koray Ergünay
- Center for Biological Threats and Special Pathogens 1 (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany. .,Department of Medical Microbiology, Virology Unit, Hacettepe University, 06100, Ankara, Turkey.
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Polat C, Ergünay K, Irmak S, Erdin M, Brinkmann A, Çetintaş O, Çoğal M, Sözen M, Matur F, Nitsche A, Öktem İMA. A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey. Infect Genet Evol 2018; 67:150-158. [PMID: 30465911 DOI: 10.1016/j.meegid.2018.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 01/10/2023]
Abstract
Orthohantaviruses (family Hantaviridae order Bunyavirales) are emerging pathogens with a significant impact on human health. They are transmitted via aerosolized excreta of rodents which also act as reservoir hosts, constituting a unique route for dispersion. Dobrava-Belgrade and Puumala orthohantaviruses have been previously reported from Anatolia, in rodents, case reports and occasional outbreaks. We have collected rodents at several locations during a surveillance study in eastern Anatolia. The specimens were morphologically-identified and various tissues were screened via a generic orthohantavirus reverse transcription polymerase chain reaction assay. DNA barcoding via mitochondrial cytochrome b sequencing was performed in rodents with detectable orthohantavirus sequences. High throughput sequencing was performed for viral genome characterization. Fifty rodents were collected and identified morphologically as Microtus spp. (96%) and Apodemus spp. (4%). Orthohantavirus sequences were detected in lung and spleen or liver tissues of 4 voles (8%), barcoded as Microtus obscurus. The virus sequences were identified as Tula orthohantavirus (TULV) and near-complete genomic segments of the prototype viral genome, tentatively named as the Tula orthohantavirus-Turkey (TULV-T), could be characterized. Putative open reading frames for viral nucleocapsid and a nonstructural protein on the S segment, glycoproteins G1 and G2 on the M segment and viral replicase on the L segment were identified on the TULV-T. Several minor sequence variants were further characterized. No evidence of recombination could be detected and pairwise comparisons displayed over 95% amino acid sequence identities to various Eurasian TULV strains. Phylogenetic analyses revealed distinct clustering of all genome segments from previously-characterized TULV strains via various approaches and models. Here, TULV-T constituted a novel lineage, forming an intermediate among Asian and European TULV lineages. This report describes the initial documentation of TULV circulation and its potential reservoir in Anatolia. The extent of virus dispersion, alternate hosts or outcomes of human exposure require elucidation.
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Affiliation(s)
- Ceylan Polat
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, 35340 Izmir, Turkey
| | - Koray Ergünay
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey.
| | - Sercan Irmak
- Balıkesir University, Science and Technology Application and Research Center, Balıkesir, Turkey
| | - Mert Erdin
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, 35340 Izmir, Turkey
| | - Annika Brinkmann
- Robert Koch Institute; Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany
| | - Ortaç Çetintaş
- Bülent Ecevit University, Faculty of Arts and Sciences, Department of Biology, Zonguldak, Turkey
| | - Muhsin Çoğal
- Bülent Ecevit University, Faculty of Arts and Sciences, Department of Biology, Zonguldak, Turkey
| | - Mustafa Sözen
- Bülent Ecevit University, Faculty of Arts and Sciences, Department of Biology, Zonguldak, Turkey
| | - Ferhat Matur
- Dokuz Eylul University, Faculty of Science, Department of Biology, Izmir, Turkey
| | - Andreas Nitsche
- Robert Koch Institute; Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany
| | - İbrahim Mehmet Ali Öktem
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, 35340 Izmir, Turkey
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Richter DC, Heininger A, Brenner T, Hochreiter M, Bernhard M, Briegel J, Dubler S, Grabein B, Hecker A, Krüger WA, Mayer K, Pletz MW, Störzinger D, Pinder N, Hoppe-Tichy T, Weiterer S, Zimmermann S, Brinkmann A, Weigand MA, Lichtenstern C. [Bacterial sepsis : Diagnostics and calculated antibiotic therapy]. Anaesthesist 2018; 66:737-761. [PMID: 28980026 DOI: 10.1007/s00101-017-0363-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The mortality of patients with sepsis and septic shock is still unacceptably high. An effective antibiotic treatment within 1 h of recognition of sepsis is an important target of sepsis treatment. Delays lead to an increase in mortality; therefore, structured treatment concepts form a rational foundation, taking relevant diagnostic and treatment steps into consideration. In addition to the assumed focus and individual risks of each patient, local resistance patterns and specific problem pathogens must be taken into account for selection of anti-infection treatment. Many pathophysiological alterations influence the pharmacokinetics of antibiotics during sepsis. The principle of standard dosing should be abandoned and replaced by an individual treatment approach with stronger weighting of the pharmacokinetics/pharmacodynamics (PK/PD) index of the substance groups. Although this is not yet the clinical standard, prolonged (or continuous) infusion of beta-lactam antibiotics and therapeutic drug monitoring (TDM) can help to achieve defined PK targets. Prolonged infusion is sufficient without TDM but for continuous infusion TDM is basically necessary. A further argument for individual PK/PD-oriented antibiotic approaches is the increasing number of infections due to multidrug resistant pathogens (MDR) in the intensive care unit. For effective treatment antibiotic stewardship teams (ABS team) are becoming more established. Interdisciplinary cooperation of the ABS team with infectiologists, microbiologists and clinical pharmacists leads not only to a rational administration of antibiotics but also has a positive influence on the outcome. The gold standards for pathogen detection are still culture-based detection and microbiological resistance testing for the various antibiotic groups. Despite the rapid investigation time, novel polymerase chain reaction (PCR)-based procedures for pathogen identification and resistance determination, are currently only an adjunct to routine sepsis diagnostics due to the limited number of studies, high costs and limited availability. In complicated septic courses with multiple anti-infective treatment or recurrent sepsis, PCR-based procedures can be used in addition to therapy monitoring and diagnostics. Novel antibiotics represent potent alternatives in the treatment of MDR infections. Due to the often defined spectrum of pathogens and the practically absent resistance, they are suitable for targeted treatment of severe MDR infections (therapy escalation).
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Affiliation(s)
- D C Richter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland.
| | - A Heininger
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - T Brenner
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - M Hochreiter
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - M Bernhard
- Zentrale Notaufnahme, Universitätsklinikum Leipzig, Leipzig, Deutschland
| | - J Briegel
- Klinik für Anästhesiologie, Klinikum der Universität München, München, Deutschland
| | - S Dubler
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - B Grabein
- Stabsstelle "Klinische Mikrobiologie und Krankenhaushygiene", Klinikum der Universität München, München, Deutschland
| | - A Hecker
- Klinik für Allgemein‑, Viszeral‑, Thorax‑, Transplantations- und Kinderchirurgie, Universitätsklinikum Gießen und Marburg, Standort Gießen, Gießen, Deutschland
| | - W A Krüger
- Klinik für Anästhesiologie und operative Intensivmedizin, Gesundheitsverbund Landkreis Konstanz, Klinikum Konstanz, Konstanz, Deutschland
| | - K Mayer
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - M W Pletz
- Zentrum für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - D Störzinger
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - N Pinder
- Apotheke des Universitätsklinikums Heidelberg, Heidelberg, Deutschland
| | - T Hoppe-Tichy
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - S Weiterer
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - S Zimmermann
- Zentrum für Infektiologie, Sektion für Krankenhaus- und Umwelthygiene, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Heidenheim, Deutschland
| | - M A Weigand
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - Christoph Lichtenstern
- Klinik für Anästhesiologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
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Benschop HOG, Guerin AJ, Brinkmann A, Dale ML, Finnie AA, Breugem WP, Clare AS, Stübing D, Price C, Reynolds KJ. Drag-reducing riblets with fouling-release properties: development and testing. Biofouling 2018; 34:532-544. [PMID: 29806493 DOI: 10.1080/08927014.2018.1469747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
The manufacture and preliminary testing of a drag-reducing riblet texture with fouling-control properties is presented. The commercial fouling-release product Intersleek® 1100SR was modified to manufacture riblet-textured coatings with an embossing technology. Hydrodynamic drag measurements in a Taylor-Couette set-up showed that the modified Intersleek® riblets reduced drag by up to 6% compared to a smooth surface. Barnacle settlement assays demonstrated that the riblets did not substantially reduce the ability of Intersleek® 1100SR to prevent fouling by cyprids of Balanus amphitrite. Diatom adhesion tests revealed significantly higher diatom attachment on the riblet surface compared to smooth Intersleek® 1100SR. However, after exposure to flow, the final cell density was similar to the smooth surface. Statically immersed panels in natural seawater showed an increase of biofilm cover due to the riblets. However, the release of semi-natural biofilms grown in a multi-species biofilm culturing reactor was largely unaffected by the presence of a riblet texture.
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Affiliation(s)
- H O G Benschop
- a Laboratory for Aero and Hydrodynamics , Delft University of Technology , Delft , the Netherlands
| | - A J Guerin
- b School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne , UK
| | - A Brinkmann
- c Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM , Bremen , Germany
| | - M L Dale
- d AkzoNobel/International Paint Ltd , Gateshead , UK
| | - A A Finnie
- d AkzoNobel/International Paint Ltd , Gateshead , UK
| | - W-P Breugem
- a Laboratory for Aero and Hydrodynamics , Delft University of Technology , Delft , the Netherlands
| | - A S Clare
- b School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne , UK
| | - D Stübing
- c Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM , Bremen , Germany
| | - C Price
- d AkzoNobel/International Paint Ltd , Gateshead , UK
| | - K J Reynolds
- d AkzoNobel/International Paint Ltd , Gateshead , UK
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Brinkmann A, Dinçer E, Polat C, Hekimoğlu O, Hacıoğlu S, Földes K, Özkul A, Öktem İMA, Nitsche A, Ergünay K. A metagenomic survey identifies Tamdy orthonairovirus as well as divergent phlebo-, rhabdo-, chu- and flavi-like viruses in Anatolia, Turkey. Ticks Tick Borne Dis 2018; 9:1173-1183. [PMID: 29728337 DOI: 10.1016/j.ttbdis.2018.04.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 11/29/2022]
Abstract
We employed a direct metagenomic approach via next-generation sequencing for a cross-sectional investigation of viruses in 10 tick pools, collected from Aegean, Mediterranean and central Anatolian locations in Turkey. Sequences from all genome segments of Tamdy orthonairovirus (family Nairoviridae) were characterized in ticks collected from a Meriones tristrami. We further obtained near-complete L and partial S segments of several tick-associated phleboviruses (family Phenuiviridae), including Tacheng tick virus 2 and a novel virus, tentatively named as the tick phlebovirus Anatolia. Partial NS5-coding region of recently-described flavi-like virus (Tacheng tick virus 8) was further detected. Moreover, near-complete and polymerase-coding regions of arthropod-associated rhabdoviruses as well as sequences closely-related to the members of the newly-proposed virus family, the Chuviridae, were characterized. Despite origins of the viral sequences could not be fully elucidated, the findings suggest the circulation of diverse arthropod and tick-associated viruses in Anatolia. Occurrence and outcome of vertebrate exposure and probable health impact of these viruses require further investigation. We also report the initial detection of Tamdy orthonairovirus, an established human pathogen, which should be included in the diagnostic workup of infections with unknown etiology.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Ender Dinçer
- Mersin University, Advanced Technology Education, Research and Application Center, 33110, Mersin, Turkey
| | - Ceylan Polat
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, 35340, Izmir, Turkey
| | - Olcay Hekimoğlu
- Hacettepe University, Faculty of Science, Department of Biology, Division of Ecology, 06800, Ankara, Turkey
| | - Sabri Hacıoğlu
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, 06110, Ankara, Turkey
| | - Katalin Földes
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, 06110, Ankara, Turkey
| | - Aykut Özkul
- Ankara University, Faculty of Veterinary Medicine, Department of Virology, 06110, Ankara, Turkey
| | - İbrahim Mehmet Ali Öktem
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, 35340, Izmir, Turkey
| | - Andreas Nitsche
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Koray Ergünay
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany; Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, 06100, Ankara, Turkey.
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Brinkmann A, Ergünay K, Radonić A, Kocak Tufan Z, Domingo C, Nitsche A. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics. PLoS Negl Trop Dis 2017; 11:e0006075. [PMID: 29155823 PMCID: PMC5714388 DOI: 10.1371/journal.pntd.0006075] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/04/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023] Open
Abstract
Background We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. Methodology An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. Principal findings The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1–10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Conclusions Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring. Viral hemorrhagic fever is a severe and potentially lethal disease, characterized by fever, malaise, vomiting, mucosal and gastrointestinal bleeding, and hypotension, in which multiple organ systems are affected. Due to modern transportation and global trade, outbreaks of viral hemorrhagic fevers have the potential to spread rapidly and affect a significant number of susceptible individuals. Thus, urgent and robust diagnostics with an identification of the causative virus is crucial. However, this is challenged by the number and diversity of the viruses associated with hemorrhagic fever. Several viruses classified in Arenaviridae, Filoviridae, and Flaviviridae families and Bunyavirales order may cause symptoms of febrile disease with hemorrhagic symptoms. We have developed and evaluated a novel method that can potentially identify all viruses and their genomic variants known to cause hemorrhagic fever in humans. The method relies on selected amplification of the target viral nucleic acids and subsequent high throughput sequencing technology for strain identification. Computer-based evaluations have revealed very high sensitivity and specificity, provided that the primer design is kept updated. Laboratory tests using several standard hemorrhagic virus strains and patient specimens have demonstrated excellent suitability of the assay in various sequencing platforms, which can achieve a definitive diagnosis in less than 3.5 hours.
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Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Koray Ergünay
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Aleksandar Radonić
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Zeliha Kocak Tufan
- Department of Infectious Diseases and Clinical Microbiology, Yıldırım Beyazıt University, Ankara, Turkey
| | - Cristina Domingo
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, ZBS 1, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- * E-mail:
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Öncü C, Brinkmann A, Günay F, Kar S, Öter K, Sarıkaya Y, Nitsche A, Linton YM, Alten B, Ergünay K. West Nile virus, Anopheles flavivirus, a novel flavivirus as well as Merida-like rhabdovirus Turkey in field-collected mosquitoes from Thrace and Anatolia. Infect Genet Evol 2017; 57:36-45. [PMID: 29128516 DOI: 10.1016/j.meegid.2017.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/04/2017] [Accepted: 11/06/2017] [Indexed: 11/30/2022]
Abstract
Mosquitoes are involved in the transmission and maintenance of several viral diseases with significant health impact. Biosurveillance efforts have also revealed insect-specific viruses, observed to cocirculate with pathogenic strains. This report describes the findings of flavivirus and rhabdovirus screening, performed in eastern Thrace and Aegean region of Anatolia during 2016, including and expanding on locations with previously-documented virus activity. A mosquito cohort of 1545 individuals comprising 14 species were collected and screened in 108 pools via generic and specific amplification and direct metagenomics by next generation sequencing. Seven mosquito pools (6.4%) were positive in the flavivirus screening. West Nile virus lineage 1 clade 1a sequences were characterized in a pool Culex pipiens sensu lato specimens, providing the initial virus detection in Aegean region following 2010 outbreak. In an Anopheles maculipennis sensu lato pool, sequences closely-related to Anopheles flaviviruses were obtained, with similarities to several African and Australian strains of this new insect-specific flavivirus clade. In pools comprising Uranotaenia unguiculata (n=3), Cx. pipiens s.l. (n=1) and Aedes caspius (n=1) mosquitoes, sequences of a novel flavivirus, distantly-related to Flavivirus AV2011, identified previously in Spain and Turkey, were characterized. Moreover, DNA forms of the novel flavivirus were detected in two Ur. unguiculata pools. These sequences were highly-similar to the sequences amplified from viral RNA, with undisrupted reading frames, suggest the occurrence of viral DNA forms in natural conditions within mosquito hosts. Rhabdovirus screening revealed sequences of a recently-described novel virus, named the Merida-like virus Turkey (MERDLVT) in 5 Cx. pipiens s.l. pools (4.6%). Partial L and N gene sequences of MERDLVT were well-conserved among strains, with evidence for geographical clustering in phylogenetic analyses. Metagenomics provided the near-full genomic sequence in a specimen, revealing an identical genome organization and limited divergence from the prototype MERDLVT isolate.
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Affiliation(s)
- Ceren Öncü
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Annika Brinkmann
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Filiz Günay
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Sırrı Kar
- Namık Kemal University, Faculty of Arts and Sciences, Department of Biology, Tekirdağ, Turkey
| | - Kerem Öter
- Istanbul University, Faculty of Veterinary Medicine, Department of Parasitology, Turkey
| | - Yasemen Sarıkaya
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Andreas Nitsche
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, MD, USA; Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bülent Alten
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Koray Ergünay
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany; Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, Turkey.
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Dinçer E, Brinkmann A, Hekimoğlu O, Hacıoğlu S, Földes K, Karapınar Z, Polat PF, Oğuz B, Orunç Kılınç Ö, Hagedorn P, Özer N, Özkul A, Nitsche A, Ergünay K. Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey. Parasit Vectors 2017; 10:335. [PMID: 28705183 PMCID: PMC5513282 DOI: 10.1186/s13071-017-2279-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/06/2017] [Indexed: 01/31/2023] Open
Abstract
Background Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens. Results A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co- infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens. Conclusions Widespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2279-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ender Dinçer
- Mersin University, Advanced Technology Education, Research and Application Center, 33110, Mersin, Turkey
| | - Annika Brinkmann
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Olcay Hekimoğlu
- Faculty of Science, Department of Biology, Division of Ecology, Hacettepe University, 06800, Ankara, Turkey
| | - Sabri Hacıoğlu
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Katalin Földes
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Zeynep Karapınar
- Faculty of Veterinary Medicine, Department of Virology, Yuzuncu Yil University, 65080, Van, Turkey
| | - Pelin Fatoş Polat
- Faculty of Veterinary Medicine, Department of Internal Medicine, Harran University, 63200,, Sanlıurfa, Turkey
| | - Bekir Oğuz
- Faculty of Veterinary Medicine, Department of Virology, Yuzuncu Yil University, 65080, Van, Turkey
| | | | - Peter Hagedorn
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Nurdan Özer
- Faculty of Science, Department of Biology, Division of Ecology, Hacettepe University, 06800, Ankara, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Andreas Nitsche
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Koray Ergünay
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany. .,Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, 06100, Ankara, Turkey.
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Ergünay K, Litzba N, Brinkmann A, Günay F, Sarıkaya Y, Kar S, Örsten S, Öter K, Domingo C, Erisoz Kasap Ö, Özkul A, Mitchell L, Nitsche A, Alten B, Linton YM. Co-circulation of West Nile virus and distinct insect-specific flaviviruses in Turkey. Parasit Vectors 2017; 10:149. [PMID: 28320443 PMCID: PMC5360070 DOI: 10.1186/s13071-017-2087-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Active vector surveillance provides an efficient tool for monitoring the presence or spread of emerging or re-emerging vector-borne viruses. This study was undertaken to investigate the circulation of flaviviruses. Mosquitoes were collected from 58 locations in 10 provinces across the Aegean, Thrace and Mediterranean Anatolian regions of Turkey in 2014 and 2015. Following morphological identification, mosquitoes were pooled and screened by nested and real-time PCR assays. Detected viruses were further characterised by sequencing. Positive pools were inoculated onto cell lines for virus isolation. Next generation sequencing was employed for genomic characterisation of the isolates. RESULTS A total of 12,711 mosquito specimens representing 15 species were screened in 594 pools. Eleven pools (2%) were reactive in the virus screening assays. Sequencing revealed West Nile virus (WNV) in one Culex pipiens (s.l.) pool from Thrace. WNV sequence corresponded to lineage one clade 1a but clustered distinctly from the Turkish prototype isolate. In 10 pools, insect-specific flaviviruses were characterised as Culex theileri flavivirus in 5 pools of Culex theileri and one pool of Cx. pipiens (s.l.), Ochlerotatus caspius flavivirus in two pools of Aedes (Ochlerotatus) caspius, Flavivirus AV-2011 in one pool of Culiseta annulata, and an undetermined flavivirus in one pool of Uranotaenia unguiculata from the Aegean and Thrace regions. DNA forms or integration of the detected insect-specific flaviviruses were not observed. A virus strain, tentatively named as "Ochlerotatus caspius flavivirus Turkey", was isolated from an Ae. caspius pool in C6/36 cells. The viral genome comprised 10,370 nucleotides with a putative polyprotein of 3,385 amino acids that follows the canonical flavivirus polyprotein organisation. Sequence comparisons and phylogenetic analyses revealed the close relationship of this strain with Ochlerotatus caspius flavivirus from Portugal and Hanko virus from Finland. Several conserved structural and amino acid motifs were identified. CONCLUSIONS We identified WNV and several distinct insect-specific flaviviruses during an extensive biosurveillance study of mosquitoes in various regions of Turkey in 2014 and 2015. Ongoing circulation of WNV is revealed, with an unprecedented genetic diversity. A probable replicating form of an insect flavivirus identified only in DNA form was detected.
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Affiliation(s)
- Koray Ergünay
- Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, Ankara, Turkey. .,Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany.
| | - Nadine Litzba
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Annika Brinkmann
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Filiz Günay
- Faculty of Sciences, Department of Biology, Division of Ecology, Hacettepe University, Ankara, Turkey
| | - Yasemen Sarıkaya
- Faculty of Sciences, Department of Biology, Division of Ecology, Hacettepe University, Ankara, Turkey
| | - Sırrı Kar
- Faculty of Arts and Sciences, Department of Biology, Namık Kemal University, Tekirdağ, Turkey
| | - Serra Örsten
- Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, Ankara, Turkey
| | - Kerem Öter
- Faculty of Veterinary Medicine, Department of Parasitology, Istanbul University, Istanbul, Turkey
| | - Cristina Domingo
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Özge Erisoz Kasap
- Faculty of Sciences, Department of Biology, Division of Ecology, Hacettepe University, Ankara, Turkey
| | - Aykut Özkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara, Turkey
| | - Luke Mitchell
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Maryland, USA
| | - Andreas Nitsche
- Robert Koch Institute, Center for Biological Threats and Special Pathogens 1 (ZBS-1), Berlin, Germany
| | - Bülent Alten
- Faculty of Sciences, Department of Biology, Division of Ecology, Hacettepe University, Ankara, Turkey
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Maryland, USA.,Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
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Ergünay K, Brinkmann A, Litzba N, Günay F, Kar S, Öter K, Örsten S, Sarıkaya Y, Alten B, Nitsche A, Linton YM. A novel rhabdovirus, related to Merida virus, in field-collected mosquitoes from Anatolia and Thrace. Arch Virol 2017; 162:1903-1911. [PMID: 28283817 DOI: 10.1007/s00705-017-3314-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 01/26/2023]
Abstract
Next-generation sequencing technologies have significantly facilitated the discovery of novel viruses, and metagenomic surveillance of arthropods has enabled exploration of the diversity of novel or known viral agents. We have identified a novel rhabdovirus that is genetically related to the recently described Merida virus via next-generation sequencing in a mosquito pool from Thrace. The complete viral genome contains 11,798 nucleotides with 83% genome-wide nucleotide sequence similarity to Merida virus. Five major putative open reading frames that follow the canonical rhabdovirus genome organization were identified. A total of 1380 mosquitoes comprising 13 species, collected from Thrace and the Mediterranean and Aegean regions of Anatolia were screened for the novel virus using primers based on the N and L genes of the prototype genome. Eight positive pools (6.2%) exclusively comprised Culex pipiens sensu lato specimens originating from all study regions. Infections were observed in pools with female as well as male or mixed-sex individuals. The overall and Cx. pipiens-specific minimal infection rates were calculated to be 5.7 and 14.8, respectively. Sequencing of the PCR products revealed marked diversity within a portion of the N gene, with up to 4% divergence and distinct amino acid substitutions that were unrelated to the collection site. Phylogenetic analysis of the complete and partial viral polymerase (L gene) amino acid sequences placed the novel virus and Merida virus in a distinct group, indicating that these strains are closely related. The strain is tentatively named "Merida-like virus Turkey". Studies are underway to isolate and further explore the host range and distribution of this new strain.
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Affiliation(s)
- Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey. .,Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany.
| | - Annika Brinkmann
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Nadine Litzba
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Filiz Günay
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Sırrı Kar
- Department of Biology, Faculty of Arts and Sciences, Namık Kemal University, Tekirdağ, Turkey
| | - Kerem Öter
- Department of Parasitology, Faculty of Veterinary Medicine, Istanbul University, Istanbul, Turkey
| | - Serra Örsten
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey
| | - Yasemen Sarıkaya
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Bülent Alten
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Andreas Nitsche
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA.,Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Ergunay K, Litzba N, Brinkmann A, Gunay F, Kar S, Oter K, Orsten S, Alten B, Nitsche A, Linton YM. Characterization of a Culex theileri flavivirus variant in field-collected mosquitoes from Turkey. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.11.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Ergünay K, Litzba N, Brinkmann A, Günay F, Kar S, Öter K, Örsten S, Sarıkaya Y, Alten B, Nitsche A, Linton YM. Isolation and genomic characterization of Culex theileri flaviviruses in field-collected mosquitoes from Turkey. Infect Genet Evol 2016; 46:138-147. [PMID: 27840255 DOI: 10.1016/j.meegid.2016.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/21/2016] [Accepted: 11/07/2016] [Indexed: 12/31/2022]
Abstract
Vector surveillance for the arthropod-borne infections has resulted in the isolation of a growing number of novel viruses, including several flavivirus strains that exclusively replicate in insects. This report describes the isolation and genomic characterization of four insect-specific flaviviruses from mosquitoes, previously collected from various locations in Turkey. C6/36 Aedes albopictus and Vero cell lines were inoculated with mosquito pools. On C6/36 cells, mild cytopathic effects, characterized as rounding and detachment, were observed in four pools that comprised female Culex theileri mosquitoes. Complete (3 isolates, 10,697 nucleotides) or near-complete (1 isolate, 10,452 nucleotides) genomic characterization was performed in these culture supernatants via next generation sequencing. All strains demonstrated high genetic similarities, with over 99% identity match on nucleotide and amino acid alignments, revealing them to be different isolates of the same virus. Sequence comparisons identified the closest relative to be the Culex theileri flavivirus (CTFV) strains, originally characterized in Portugal. Phylogenetic analyses demonstrated that the isolates remained distinct as a cluster but formed a monophyletic group with CTFV strains, and shared a common ancestor with Quang Binh or related Culex flaviviruses. The organization of the viral genome was consistent with the universal flavivirus structure and stem-loops; conserved motifs and imperfect tandem repeats were identified in the non-coding ends of the viral genomes. A potential ribosomal shifting site, resulting in the translation of an additional reading frame, was detected. The deduced viral polyprotein comprised 3357 amino acids and was highly-conserved. Amino acid variations, presumably associated with adaptive environmental pressures, were identified. These isolates comprise the first fully characterized insect-specific flaviviruses in Turkey. Their impact on West Nile virus circulation, which is also endemic in the study region, remains to be explored.
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Affiliation(s)
- Koray Ergünay
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, Turkey; Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany.
| | - Nadine Litzba
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany
| | - Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany
| | - Filiz Günay
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Sırrı Kar
- Namık Kemal University, Faculty of Arts and Sciences, Department of Biology, Tekirdağ, Turkey
| | - Kerem Öter
- Istanbul University, Faculty of Veterinary Medicine, Department of Parasitology, Istanbul, Turkey
| | - Serra Örsten
- Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Ankara, Turkey
| | - Yasemen Sarıkaya
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Bülent Alten
- Hacettepe University, Faculty of Sciences, Department of Biology, Division of Ecology, Ankara, Turkey
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Berlin, Germany
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA; Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Brinkmann A, Röhr AC, Köberer A, Fuchs T, Preisenberger J, Krüger WA, Frey OR. [Therapeutic drug monitoring and individual dosing of antibiotics during sepsis : Modern or just "trendy"?]. Med Klin Intensivmed Notfmed 2016; 113:82-93. [PMID: 27624768 DOI: 10.1007/s00063-016-0213-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 01/25/2023]
Abstract
Pharmacokinetic variability of anti-infective drugs due to pathophysiological changes by severe sepsis and septic shock is a well-known problem for critically ill patients resulting in suboptimal serum and most likely tissue concentrations of these agents.To cover a wide range of potential pathogens, high concentrations of broad spectrum anti-infectives have to reach the site of infection. Microbiological susceptibility testing (susceptible, intermediate, resistant) don't take the pharmacokinetic variability into account and are based on data generated by non-critically ill patients. But inter-patient variability in distribution and elimination of anti-infective drugs in ICU patients is extremely high and also highly unpredictable. Drug clearance of mainly renally eliminated drugs and thus the required dose can differ up to 10-fold due to the variability in renal function in patients with severe infections. To assure a timely and adequate anti-infective regime, individual dosing and therapeutic drug monitoring (TDM) seem to be appropriate tools in the setting of pathophysiological changes in pharmacokinetics (PK) and pharmakodynamics (PD) due to severe sepsis. In the case of known minimal inhibitory concentration, PK/PD indices (time or peak concentration dependent activity) and measured serum level can provide an optimal target concentration for the individual drug and patient.Modern anti-infective management for ICU patients includes more than the choice of drug and prompt application. Individual dosing, optimized prolonged infusion time and TDM give way to new and promising opportunities in infection control.
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Affiliation(s)
- A Brinkmann
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustraße 100, 89522, Heidenheim, Deutschland.
| | - A C Röhr
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
| | - A Köberer
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustraße 100, 89522, Heidenheim, Deutschland
| | - T Fuchs
- Klinik für Anästhesie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, Schlosshaustraße 100, 89522, Heidenheim, Deutschland
| | | | - W A Krüger
- Klinik für Anästhesiologie und Operative Intensivmedizin, Klinikum Konstanz, Konstanz, Deutschland
| | - O R Frey
- Apotheke, Klinikum Heidenheim, Heidenheim, Deutschland
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Brinkmann A, Braun JP, Riessen R, Dubb R, Kaltwasser A, Bingold TM. [Quality assurance concepts in intensive care medicine]. Med Klin Intensivmed Notfmed 2015; 110:575-80, 582-3. [PMID: 26497132 DOI: 10.1007/s00063-015-0095-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/19/2015] [Indexed: 11/25/2022]
Abstract
Intensive care medicine (ICM) is characterized by a high degree of complexity and requires intense communication and collaboration on interdisciplinary and multiprofessional levels. In order to achieve good quality of care in this environment and to prevent errors, a proactive quality and error management as well as a structured quality assurance system are essential. Since the early 1990s, German intensive care societies have developed concepts for quality management and assurance in ICM. In 2006, intensive care networks were founded in different states to support the implementation of evidence-based knowledge into clinical routine and to improve medical outcome, efficacy, and efficiency in ICM. Current instruments and concepts of quality assurance in German ICM include core intensive care data from the data registry DIVI REVERSI, quality indicators, peer review in intensive care, IQM peer review, and various certification processes. The first version of German ICM quality indicators was published in 2010 by an interdisciplinary and interprofessional expert commission. Key figures, indicators, and national benchmarks are intended to describe the quality of structures, processes, and outcomes in intensive care. Many of the quality assurance tools have proved to be useful in clinical practice, but nationwide implementation still can be improved.
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Affiliation(s)
- A Brinkmann
- Klinik für Anästhesiologie, operative Intensivmedizin und spezielle Schmerztherapie, Klinikum Heidenheim, gGmbH, Schlosshaustraße 100, 89522, Heidenheim, Deutschland.
| | - J P Braun
- Klinik für Anästhesie, Intensivmedizin und Schmerztherapie, Helios Klinikum Hildesheim, Hildesheim, Deutschland
| | - R Riessen
- Internistische Intensivstation, Department für Innere Medizin, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - R Dubb
- Akademie der Kreiskliniken Reutlingen, Kreiskliniken Reutlingen GmbH, Reutlingen, Deutschland
| | - A Kaltwasser
- Akademie der Kreiskliniken Reutlingen, Kreiskliniken Reutlingen GmbH, Reutlingen, Deutschland
| | - T M Bingold
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Frankfurt, Frankfurt/Main, Deutschland
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Abstract
This protocol can rapidly and reliably detect viruses during disease outbreaks and for detection studies. Sixty percent of emerging viruses have a zoonotic origin, making transmission from animals a major threat to public health. Prompt identification and analysis of these pathogens are indispensable to taking action toward prevention and protection of the affected population. We quantifiably compared classical and modern approaches of virus purification and enrichment in theory and experiments. Eventually, we established an unbiased protocol for detection of known and novel emerging viruses from organ tissues (tissue-based universal virus detection for viral metagenomics [TUViD-VM]). The final TUViD-VM protocol was extensively validated by using real-time PCR and next-generation sequencing. We could increase the amount of detectable virus nucleic acids and improved the detection of viruses <75,000-fold compared with other tested approaches. This TUViD-VM protocol can be used in metagenomic and virome studies to increase the likelihood of detecting viruses from any biological source.
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Nieuwland M, Ruizendaal L, Brinkmann A, Kroon-Batenburg L, van Hest JCM, Löwik DWPM. A structural study of the self-assembly of a palmitoyl peptide amphiphile. Faraday Discuss 2013; 166:360-79. [DOI: 10.1039/c3fd00055a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kampschulte M, Schwab J, Brinkmann A, Gunkel I, Klaus M, Krombach GA, Langheinrich AC. Nano-CT zur Charakterisierung atherosklerotischer Plaque – Techniken und Ergebnisse. ROFO-FORTSCHR RONTG 2012. [DOI: 10.1055/s-0032-1329781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kohl C, Lesnik R, Brinkmann A, Ebinger A, Radonić A, Nitsche A, Mühldorfer K, Wibbelt G, Kurth A. Isolation and characterization of three mammalian orthoreoviruses from European bats. PLoS One 2012; 7:e43106. [PMID: 22905211 PMCID: PMC3419194 DOI: 10.1371/journal.pone.0043106] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/17/2012] [Indexed: 12/16/2022] Open
Abstract
In recent years novel human respiratory disease agents have been described in South East Asia and Australia. The causative pathogens were classified as pteropine orthoreoviruses with strong phylogenetic relationship to orthoreoviruses of flying foxes inhabiting these regions. Subsequently, a zoonotic bat-to-human transmission has been assumed. We report the isolation of three novel mammalian orthoreoviruses (MRVs) from European bats, comprising bat-borne orthoreovirus outside of South East Asia and Australia and moreover detected in insectivorous bats (Microchiroptera). MRVs are well known to infect a broad range of mammals including man. Although they are associated with rather mild and clinically unapparent infections in their hosts, there is growing evidence of their ability to also induce more severe illness in dogs and man. In this study, eight out of 120 vespertilionid bats proved to be infected with one out of three novel MRV isolates, with a distinct organ tropism for the intestine. One isolate was analyzed by 454 genome sequencing. The obtained strain T3/Bat/Germany/342/08 had closest phylogenetic relationship to MRV strain T3D/04, isolated from a dog. These novel reoviruses provide a rare chance of gaining insight into possible transmission events and of tracing the evolution of bat viruses.
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Affiliation(s)
- Claudia Kohl
- Robert Koch Institute, Centre for Biological Security 1, Berlin, Germany.
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Kurth A, Kohl C, Brinkmann A, Ebinger A, Harper JA, Wang LF, Mühldorfer K, Wibbelt G. Novel paramyxoviruses in free-ranging European bats. PLoS One 2012; 7:e38688. [PMID: 22737217 PMCID: PMC3380927 DOI: 10.1371/journal.pone.0038688] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 05/08/2012] [Indexed: 11/25/2022] Open
Abstract
The zoonotic potential of paramyxoviruses is particularly demonstrated by their broad host range like the highly pathogenic Hendra and Nipah viruses originating from bats. But while so far all bat-borne paramyxoviruses have been identified in fruit bats across Africa, Australia, South America, and Asia, we describe the detection and characterization of the first paramyxoviruses in free-ranging European bats. Moreover, we examined the possible impact of paramyxovirus infection on individual animals by comparing histo-pathological findings and virological results. Organs from deceased insectivorous bats of various species were sampled in Germany and tested for paramyxovirus RNA in parallel to a histo-pathological examination. Nucleic acids of three novel paramyxoviruses were detected, two viruses in phylogenetic relationship to the recently proposed genus Jeilongvirus and one closely related to the genus Rubulavirus. Two infected animals revealed subclinical pathological changes within their kidneys, suggestive of a similar pathogenesis as the one described in fruit bats experimentally infected with Hendra virus. Our findings indicate the presence of bat-born paramyxoviruses in geographic areas free of fruit bat species and therefore emphasize a possible virus–host co-evolution in European bats. Since these novel viruses are related to the very distinct genera Rubulavirus and Jeilongvirus, a similarly broad genetic diversity among paramyxoviruses in other Microchiroptera compared to Megachiroptera can be assumed. Given that the infected bats were either found in close proximity to heavily populated human habitation or areas of intensive agricultural use, a potential risk of the emergence of zoonotic paramyxoviruses in Europe needs to be considered.
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Affiliation(s)
- Andreas Kurth
- Robert Koch Institute, Centre for Biological Security, Berlin, Germany.
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Bartels U, Brinkmann A, Ziegler M, Schmidt A. Eine schwere Aufgabe – adipöse Patienten in der Notfallmedizin. Notf Rett Med 2012. [DOI: 10.1007/s10049-011-1508-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Böer U, Brinkmann A, Jansen H, Martin Y, Haverich A, Wilhelmi M. Set-up and evaluation of an automated system for the efficient decellularization of equine carotid arteries as bioartificial vascular grafts. BIOMED ENG-BIOMED TE 2012. [DOI: 10.1515/bmt-2012-4098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Birkenheuer G, Blunk D, Breuers S, Brinkmann A, dos Santos Vieira I, Fels G, Gesing S, Grunzke R, Herres-Pawlis S, Kohlbacher O, Kruber N, Krüger J, Lang U, Packschies L, Müller-Pfefferkorn R, Schäfer P, Schmalz HG, Steinke T, Warzecha KD, Wewior M. MoSGrid – a molecular simulation grid as a new tool in computational chemistry, biology and material science. J Cheminform 2011. [PMCID: PMC3083568 DOI: 10.1186/1758-2946-3-s1-p14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brinkmann A, Moritz R, Schneck E, Kline TL, Eaker DR, Gerlach SV, Bohle RM, Langheinrich AC, Lerman LO, Ritman EL. 3-Dimensional Structural and Volumetric Analysis of Glomeruli in Porcine Kidneys with Renal Artery Stenosis using Nano-Computed Tomography. ROFO-FORTSCHR RONTG 2011. [DOI: 10.1055/s-0031-1279297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kampschulte M, Gunkel I, Stieger P, Sedding D, Gerlach SV, Brinkmann A, Ritman EL, Langheinrich AC. Thalidomide inhibits Vasa Vasorum Neovascularization in Aortas of ApoE-/-/LDL-/- Double Knockout Mice. ROFO-FORTSCHR RONTG 2011. [DOI: 10.1055/s-0031-1279105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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