Research in Groningen: Pronkjewail – second pillar.
This is the second part of a four-part piece (read the first part here).
Pronkjewail is a Doctoral Training Programme co-funded by Marie Skłodowska-Curie Actions*. This is a programme where 16 international PhD students have come to the University Medical Center Groningen at the University of Groningen to do research. All PhD students have opportunities to go on different secondments in academia and industry, and the overall goal of the project is ‘protecting patients with enhanced susceptibility to infections’. Our 16 projects are divided into four pillars: vaccines and primary prevention (1), personalized detection and infection prevention (2), iatrogenic influence on the microbiome (3) and personalized therapy/stewardship (4).
We asked all Pronkjewail PhD students to describe their research in their own words through two questions: What is your research about? and What could potentially be the future impact of your research? MindMint will be publishing the answers of PhD students working in each of the pillars.
Use of Next generation Sequencing in detection of micro-organisms and antimicrobial resistance genes
The majority of conventional and culture independent diagnostic techniques target several specific organisms and therefore only yield very limited information. Recent technical advances made it possible to analyze the whole microbiome that is present within a clinical sample indiscriminately. That way all pathogens can not only be detected but also characterized (antibiotic resistance, virulence factors, viral recombination etc.). Those broad and untargeted “shotgun” approaches can also incorporate host based diagnostics and have the potential to answer almost all clinical questions within one assay.
Rapid personalized molecular detection and cost/benefit in patient care
During my PhD me and my group will perform several tests, from routine diagnostics to epidemiology where we track trends in what was actually found. We also perform basic research which involves a more targeted detection and assay development. One of my main aims of my project is to development techniques and strategies which will aid rapid characterization of picornaviruses. Picornaviruses represent a large family of viruses such as enterovirus or hepatitis A virus and can cause a wide range of clinical presentations.
In terms of impact, my work could help towards a more optimized molecular workflow in diagnostics and enable more real-time detection and epidemiology. This has an impact not only in patient management but for outbreak preparedness and response.
Rapid direct detection of micro-organisms and resistance determinants using innovative approaches
My research topic is development of new approaches to speed up the process of microbial identification and prediction of the relevant resistance determinants. Gold standard culture-based methods are rather slow and current rapid molecular tests only cover a few resistance determinants. However, early administration and modification of an appropriate antimicrobial therapy is vital for a patient. We are aiming to improve the quality and cost-effectiveness of health care as well as reduce antimicrobial resistance selection by developing new diagnostic approaches to be implemented in microbial diagnostic laboratories.
One of the approaches I focus on is using next generation sequencing (NGS) technologies for diagnosis directly from patient material. This approach will be eliminating the need for time-consuming culture-based methods and other molecular tests (PCR) in some situations. Basically, we extract all the genetic material from a patient sample (blood, serum, urine, sputum e.g.) and sequence it to identify the microbial genomes through a high abundant of host human genome.
SAPS II: Exploring the use of procalcitonin as a marker of infection resolution in critically ill
Several trials have shown that daily procalcitonin (PCT) monitoring helps to identify a patient may have systemic bacterial infection that can become life-threatening. Moreover, decreasing PCT levels over time in a person being treated for a bacterial infection indicate a response to therapy. But still PCT measurements is not part of the routine clinical care in the Netherlands. My research mostly is focused on implementation of PCT in the intensive care units.
The key hypothesis to be tested in this research is that PCT will decrease the antibiotic usage of patients by implementation in normal care.
Identification of Multi-Drug-resistant Organisms (MDRO) in Refugees
During the past few decades, ‘smart’ microbes that cannot be killed with the common antibiotics, have been causing infections and making the life of clinicians increasingly more difficult. Such microbes may prefer certain conditions and countries more than others and can use humans as carriers to overcome geographical borders and travel with them.
My research is focusing on potential relocation of these microbes through asylum seekers populations. Hopefully, investigating microbial movement will lead to the ability of predicting their moves and be one step ahead of them.
* Grant Agreement number: 713660 — PRONKJEWAIL — H2020-MSCA-COFUND-2015