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Interview with PhD student Juan Pablo Rodriguez Ruiz

Interview with PhD student Juan Pablo Rodriguez Ruiz

Read our interview with PhD student Juan Pablo Rodriguez Ruiz at the Laboratory of Medical Microbiology at the University of Antwerp. He discusses his work with Work Package 2 within Value-Dx, his future tasks and more.













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.

More interviews

Does diagnostic testing always decrease antibiotics prescriptions?

Does diagnostic testing always decrease antibiotics prescriptions?

In August 2022, VALUE-Dx published a new article in the European Journal of Health Economics with the following title: ‘Does diagnostic testing always decrease antibiotics prescriptions?’. The conclusion of this scientific paper is that we should be very careful when we assert that point-of-care diagnostic testing (POCT) reduces antibiotics prescriptions as there are situations in which the opposite effect occurs.

Why POCT?
Empiric prescription as a treatment for infectious diseases in community care settings has caused antibiotics to be overprescribed, resulting in an increase of antimicrobial resistance (AMR). In order to reduce antibiotics prescription, point-of-care diagnostic testing (POCT) has been suggested.

In this new VALUE-Dx article, a stylised static theoretical economic model was used to analyse whether POCT always decreases antibiotics prescriptions. The interaction of a group of doctors who differ in their level of concern about AMR when prescribing with a firm selling a POCT was taken into consideration. The price set by the manufacturer and doctors’ decision to employ POCT was characterised.

Results of the study
It is widely accepted that the use of diagnostic testing to guide antibiotics prescription in community care settings reduces the number of antibiotics prescriptions. However, the model used in this article shows that we should be very careful with recommending the use of POCT to reduce antibiotics prescriptions as we may end up with the opposite result.

In fact, the number of antibiotics prescriptions is not always lower. It depends on the distribution of the doctors’ concern about AMR as there is a proportion of doctors who use POCT and then prescribe antibiotics, while other doctors change their prescribing behaviour after using POCT. They stop giving antibiotics to patients who do not benefit from them. When the proportion of patients who need antibiotic treatment is higher than the proportion of doctors who use POCT and stop prescribing unnecessary antibiotics, the number of antibiotics prescriptions is larger.

These analyses convey the message that we should be very careful when we assert that POCT reduces antibiotics prescriptions as there are situations in which the contrary effect is produced.

You can read the publication here.

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