ESR 2.1
Use of Next Generation Sequencing in detection of micro-organisms and anti-microbial resistance genes

Project

Next generation sequencing is more and more used in routine clinical microbiology and infection prevention to determine the genetic relationship between pathogens (used to guide infection prevention measures) and for the molecular detection and further characterization of (emerging) pathogens. This includes analyses for revealing (new) antibiotic resistance mechanisms and for determining the virulence of pathogens resulting in improved risk assessment and treatment of patients. In this project a (RNA)-metagenomic approach will be used and optimized to identify pathogens present in clinical samples. Furthermore, it will focus on studying interactions between pathogens and their host resulting in a method to differentiate between colonization (presence of a pathogen) and infection of a patient with the pathogen. In addition, based on comparing whole genomes of pathogens, tailor-made diagnostic tests will be developed used for specific detection of outbreak and or virulent strains. The candidate will develop skills in Next Generation (deep) Sequencing and big data analyses.

Supervisors

  • Dr. Silke Peter, Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany, » Link
  • Dr. John W. Rossen, Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands » Link

Collaborations

Dr. Robert Schlaberg, ARUP laboratories, University of Utah, Utah, US and Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands, Check-points, Wageningen, The Netherlands

Relevant publications

  1. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, et al. Unbiased Detection of Respiratory Viruses Using RNA-seq-Based Metagenomics: A Systematic Comparison to A Commercial PCR Panel. J Clin Microbiol [Internet]. 2016;(January):JCM.03060–15.
  2. Willmann M, El-Hadidi M, Huson DH, Schütz M, Weidenmaier C, Autenrieth IB, et al. Antibiotic selection pressure determination through sequence-based metagenomics. Antimicrob Agents Chemother. 2015;59(12):7335–45.
  3. Zhou K, Lokate M, Deurenberg RH, Tepper M, Arends JP, Raangs EGC, et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum beta-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016 Feb 11;6.

Keywords

next-generation sequencing, metagenomics, anti-microbial resistance