Juan Pablo Rodriguez Ruiz is a 27-year-old PhD student at the Laboratory of Medical Microbiology of the University of Antwerp. He studies the microbiome of patients suffering from Respiratory Tract Infections and the effect of antibiotic intake in these patients within the VALUE-Dx project. Juan Pablo has a Bachelor in Biotechnology at Universidad Pablo de Olavide (Sevilla) and a Master in Microbiology at Universidad de Granada.
What does your work for VALUE-Dx entail?
Juan Pablo: I’m part of Work Package 2 (WP2), the microbiology side of the VALUE-Dx project. We mainly perform substudies derived from the main trials ADEQUATE-paediatric and PRUDENCE in WP4. Within these substudies there is a metagenomics part, revolving around the microbiome related to the antibiotic treatments in the trials. There is also another part revolving around biomarkers but I’m not involved in that. Lastly, we biobank the samples from the trials. My main role is to perform the metagenomics of the microbiology studies in the lab. We sequence the DNA of the samples we receive from the trials and evaluate the effect of the antibiotic treatments.
How long have you been working on the project?
Juan Pablo: Since the start of VALUE-Dx, so about four years ago. In the beginning, I spent a month at the University of Edinburgh, one of the VALUE-Dx partners. They are creating a technical roadmap with recommendations for short- and long-term goals to help companies and research institutions prioritize investment decisions in the field of CA-ARTI diagnostics. In Edinburgh, I did research into companies that are developing new diagnostic tests for respiratory tract infections (RTI).
Currently, at the Laboratory of Medical Microbiology at the University of Antwerp, my job is to make sure that everything is ready for when the samples arrive. I take care of setting up the DNA extraction and sequencing protocols, the bioinformatics pipeline, etc.
What upcoming tasks do you have for VALUE-Dx?
Juan Pablo: We are in the process of receiving the samples from the trials. Once we receive them, we can start the lab work. In ADEQUATE-paediatric, the patients are children presenting with community-acquired pneumonia in the emergency room. They are randomised to either undergo the diagnostic tests or the usual care. With regards to the substudy in which I am involved, we ask for oropharyngeal samples at the randomization and one month later and we want to see whether the antibiotics that have been prescribed have an effect on the microbiome and the resistance in the oropharynx.
PRUDENCE works with patients in long term care facilities. If these patients develop respiratory tract infections they get tested, depending on what group they are randomised in. For the substudy, we take additional samples in order to see the effect of antibiotic prescriptions.
What did you find most challenging about the project? What has been the most exciting?
Juan Pablo: Coordinating a multi-centre, international study is of course very challenging. In my case specifically, the delay of the samples due to the COVID-19 pandemic posed a big challenge. The start of the trial was delayed for more than one year. Now, the recruitment is ongoing so, step by step, we’re getting there. On the other hand, in other work packages, there has already been a lot of work done.
For me, it was very exciting to get everything ready for when the samples arrive. This includes preparing the right protocols, sequencing, bioinformatic tools, etc. That was also the upside of the delay, we had more time to put everything together with great care.
Juan Pablo graduated as a Bachelor in Biotechnology at Universidad Pablo de Olavide (Seville) in 2016 and as a Master in Microbiology at Universidad de Granada in 2018. As a PhD student at the Laboratory of Medical Microbiology, he studies the microbiome of patients suffering from Respiratory Tract Infections and the effect of antibiotic intake in these patients.
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