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Juraschek K, Borowiak M, Tausch SH, et al. Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal . Microorganisms. 2021;9(3)doi: 10.3390/microorganisms9030598.
Juraschek, K., Borowiak, M., Tausch, S. H., Malorny, B., Käsbohrer, A., Otani, S., Schwarz, S., Meemken, D., Deneke, C., & Hammerl, J. A. (2021). Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal . Microorganisms, 9(3), . https://doi.org/10.3390/microorganisms9030598
Juraschek, Katharina, et al. "Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal ." Microorganisms vol. 9,3 (2021). doi: https://doi.org/10.3390/microorganisms9030598
Juraschek K, Borowiak M, Tausch SH, Malorny B, Käsbohrer A, Otani S, Schwarz S, Meemken D, Deneke C, Hammerl JA. Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal . Microorganisms. 2021 Mar 14;9(3). doi: 10.3390/microorganisms9030598. PMID: 33799479; PMCID: PMC8000739.
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Microorganisms. 2021 Mar 14;9(3). doi: 10.3390/microorganisms9030598.

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

Microorganisms

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

Affiliations

  1. Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany.
  2. Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany.
  3. Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
  4. DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark.
  5. Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany.
  6. Institute of Food Safety and Food Hygiene, Working Group Meat Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany.

PMID: 33799479 PMCID: PMC8000739 DOI: 10.3390/microorganisms9030598

Abstract

Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in

Keywords: AMR; hybrid assembly; long-read sequencing; mobile genetic elements; qnrS; short-read sequencing

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