Jena University Hospital: PhD position for 36 months, 65%

Announcment: PhD position for 36 months, 65%

Project: Development of a modular multiplex detection system for plasmid-based antibiotic resistance monitoring

Topic: Microbial antibiotic resistance is an increasing worldwide problem for health care. Resistance is disseminated via self-replicating mobile plasmids that can be exchanged between different bacterial species. While the available surveillance systems primary track the phenotypic  resistance epidemiology in hospitals, resistnace genes are exchanged between the pathogens via natural plasmids that are not detected, especially in the environment. These reservoirs, as well as the epidemiology behind them, are currently not monitored, but they represent important parts of the overall epidemiology and more importantly, the control of resistance spread. Therefore, this collaborative project aims to develop a plasmid-based antibiotic resistance monitoring. It is an innovative plasmid isolation method that uses conserved sequence sections within the highly variable plasmids to specifically separate the incompatibility groups. This method will be integrated in a microfluidic chip. Resistance testing will be then carried out using a highly innovative and label-free plasmonic method, which will be integrated into the microfluidic chip. The collaborative project will be carried out by experts in the respective field in modules that are closely interlinked and coordinated by the industrial partner, who carries out the integration of the entire system.

Project period: 01.01.2019- 31.12.2021 (36 months)

Alliance partners:

  • Coordinator: SIOS Meßtechnik GmbH
  • Jena University Hospital, Institute of Infectious Diseases and Infection Control
  • Leibniz Institute for Photonic Technologies e.V.
  • Milendo GmbH

Task: The project is modular and within the scope of the doctoral thesis the module 1 will be in the focus. Here, suitable capture probes for Gram-negative plasmids will be reconstructed. The idea builds on the experience of the UKJ in the targeted enrichment ("fishing") of nucleic acids. In the process, the plasmids are bound (fished) by means of special highly conserved sequence segments which are located in the mob and rep regions. These areas have sufficient sequence homology within the incompatibility groups to bind to the probes and thus the plasmids can be specifically captured and isolated from complex media. Of the 27 incompatibility groups (Inc) in Gram-negative bacteria, which are not equally frequent, only 10 of the most prevalent Inc groups will be targeted as specific binding partners. These conserved target sequences will be refined by an intensive sequence analysis of the open genome databases. The 'fishing' will be optimized in module 1 step by step on laboratory scale on chracterized isolates. Here, hybridization protocols for the capture probes (temperature, saline concentrations, or capture probe concentration) and, if necessary, capture probes must be modified to find the highest catcher efficiency conditions for all capture probes where the fishing protocol can be kept as simple as possible. In addition, chemical modifications of the capture probes may be necessary to chemically couple and permanently bind the plasmids to the capture probes after hybridization. Accordingly, the efficiency of various processing operations that will later be necessary for the detection of the resistance genes, such as specific and nonspecific amplifications, if necessary a specific chemical labeling of the amplificates, will also be investigated.

Through close integration with the cooperation partners in the other modules, the doctoral student will also gain insights into label-free detection of the resistance genes by means of localized surface plasmon resonance (LSPR), in sample preparation from complex media (such as blood or urine) and microfluidic technology.

Requirements for application:

  • Master's degree in science, preferably in biology, molecular medicine, biochemistry or biotechnology (or equivalent)
  • Good knowledge of microbiological, molecular biological and bioinformatics work is a prerequisite and should be documented in the CV by appropriate course participation or work

Contact person: Send your complete application documents (motivation letter, certificates, CV including practical laboratory experience) by e-mail to Dr. Oliwia Makarewicz: oliwia.makarewicz@med.uni-jena.de