AMR expert interview with Dr. Füsun Can

AMR expert interview with Dr. Füsun Can

Meet Dr. Füsun Can, a medical doctor and professor in Istanbul. She leads a multidisciplinary team focused on antibiotic resistance research. With expertise in virology and a commitment to collaborative efforts, Dr. Can’s work extends beyond the laboratory, aiming to address emerging infectious disease challenges across Turkey.

Can you introduce yourself and describe your role in the AMR field?

I’m a medical doctor and a professor in medical microbiology. Currently, I am the laboratory director of  the Koc University Research Center for Infectious Diseases in Istanbul. One of our laboratory units is focused on research in antibiotic resistance and we collaborate with different centres throughout Turkey, conducting multicenter studies. One of our research topics, for example, is biofilm related infections and we work together with other scientists from our university such as engineers and chemists to find new strategies to combat these infections. We also explore the efficiency of diagnostic tests, especially molecular and multiplex PCR tests.

What are some challenges that you are currently facing?

Antibiotic resistance and the treatment of resistant infections is not an isolated problem. We should look into the virulence of bacteria and the immune response of bacterial virulence factors as well. By focusing on these aspects together, we can uncover new strategies to combat resistant bacterial infections. In my laboratory, we’re delving into studies on pathogenesis and virulence factors.

Why should people be concerned about AMR?

Antibiotic resistance is concerning because of several reasons. It poses a significant global health threat, leading to issues such as bacterial infections with increased severity and fatality rates. In Turkey, being a critical geographical bridge between Asia and Europe, there’s a unique challenge with the spread of resistance genes from both regions.

On top of that, inappropriate antibiotic use and limited access to rapid diagnostics contribute to the growing problem. Altogether, this causes higher fatality rates and puts economic strain on the public and the government. High carbapenem-resistant rates, for example, complicate possible treatments which in a lot of cases ends up in expensive combination therapies and delayed results. Another example is the resistance to common antibiotics like Ciprofloxacin for urinary tract infections, so there is a growing concern for treatment failure.

Do you believe the Turkish population is aware of these risks?

Among the educated population, there’s a growing awareness of the risks associated with antibiotic resistance and the inappropriate use of antibiotics. However, this awareness is lacking among the non-educated groups of Turkish society. In a lot of cases, we see a strong preference for injectable antibiotics over oral ones, even in minor infections. Especially the overuse of antibiotics for respiratory infections remains a problem. Part of the cause is the difficulty to diagnose those infections and the expensive diagnostic tests.

What is the expected impact of the work you’re doing?

In my laboratory, we collaborate closely with clinicians to address emerging infectious disease challenges in our country and region. Embracing a ‘One Health’ approach, we engage infectious disease specialists, veterinarians, and agricultural professionals to monitor antibiotic resistance across Turkey. This collaborative effort aims to contribute significantly to the prevention and control of AMR. Additionally, our team conducts clinical research focusing on antibiotic resistance and antimicrobial stewardship. Through initiatives such as AMS programs and evaluating the impact of rapid diagnostic systems on patient outcomes, we aim to improve clinicians’ ability to manage patients effectively.

One of the aims of VALUE-Dx is to demonstrate the value of diagnostics to change the antibiotics prescribing behaviour. Can you comment on this?

Rapid diagnostic systems are crucial yet their high cost remains a barrier, especially for countries like Turkey with limited economic resources. Cheaper diagnostic tools are essential, but ensuring their effectiveness across different regions, including those with specific resistance genes, is equally vital. It’s essential that diagnostic tools developed by companies in Europe or the United States address a broader range of resistance issues to have a meaningful impact globally.

How did the COVID-19 pandemic impact the research on AMR?

During the COVID-19 pandemic, our research laboratory faced significant shifts in focus and resources. The launch of our lab was originally delayed due to financial factors but because of the start of the pandemic, new funds became available. So, we were able to conduct vital COVID-19 studies. However, travel restrictions and lab closures delayed our AMR studies. Similarly, across Turkey, microbiologists redirected their efforts towards COVID-19 diagnostics, with routine laboratories repurposed for testing. Despite these challenges, we remain committed to resuming our AMR projects and anticipate catching up on our schedule within the coming months.


On the positive side, there has been a significant increase in awareness regarding the appropriate use of antibiotics for respiratory infections. Previously, all pneumonia cases were typically treated with antibiotics, but now there’s recognition that viral infections can also cause pneumonia. This shift has led to improved understanding among both the general population and the medical community, with people now aware of viral pneumonia and the importance of distinguishing between bacterial and viral infections. Additionally, the pandemic has contributed to greater public knowledge about PCR tests, thanks to educational programs and discussions on television.

Prof. Füsun Can is a professor in the department of Medical Microbiology at the Koc University, School of Medicine. She is also the laboratory director of the Koc University Research Center for Infectious Diseases in in Koç University. Her research interests span antimicrobial resistance and emerging diseases. Much of her work on molecular epidemiology of antibiotic resistance and host-pathogen interactions. She is editor of books on Emerging Infectious Diseases: Clinical Case Studies (2014, Elsevier, awarded by British Medical Association as the book of the year), and Antimicrobial Stewardship (Elsevier, 2018). She is a member of ESCMID (European Society of Clinical Microbiology and Infectious Diseases) and American Society for Microbiology (ASM).

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AMR expert interview with Dr. Agnes Sonnevend

AMR expert interview with Dr. Agnes Sonnevend

Read our interview with Dr. Agnes Sonnevend from the Pécs University Hospital in Hungary. Dr. Sonnevend elaborates on the importance and challenges of tackling AMR, her role in this and more.

Can you introduce yourself and tell us about your role in the AMR field?

I am Agnes Sonnevend, head of the Diagnostic Microbiology Services at University of Pécs University Hospital in Hungary, which has over 1400 beds. We treat patients in the fields of haematology, oncology, solid organ transplantation, both children and adults. Previously, I did research in the Middle East on antimicrobial resistant bacteria, mostly gram-negatives, and molecular epidemiology. I’m continuing this work in Hungary with the help of my PhD-students and colleagues. I am also part of the National Antimicrobial Resistance Testing Committee, which aims to improve the overall quality of antimicrobial susceptibility testing in Hungary and adhere to the EUCAST.  

What are some challenges that you are currently facing?

In the committee, we are currently discussing selective reporting and whether or not to suppress certain antibiotics to decrease their use in outpatient settings. There is also a debate ongoing about accidentally discovered multidrug-resistant organism carriers. In my opinion, this is a pressing issue and we need to figure out how to approach it. 

Why should people be concerned about AMR?

The most important aspect of AMR is that it’s not only a current problem, but it will also gravely affect generations to come. In Europe, antibiotics are not over-the-counter available, however, in most other parts of the world this unfortunately is the case. This means that a lot of people take antibiotics even if they have a simple cold or hay fever. Doctors also need to be selective when it comes to prescribing antibiotics and think about future patients who will potentially need antibiotics for more serious infections. If the widespread over-use of antibiotics continues, then our children and the future generations will not be able to take effective antibiotics. Even simple infections could become life-threatening.

What is the expected impact of the work you’re doing?

At the Diagnostic Microbiology Services of the University Hospital, we perform molecular testing for multi-resistant organisms, often genome-sequence based. In this case, it’s easier to pinpoint connections and determine the necessary actions to be taken. Thanks to this, our hospital is able to handle antimicrobial resistance well. I advocate for providing funding to all hospitals so that they can perform this testing as well. Our National Center of Epidemiology carries out these tests, but the turnover time is long. When hospitals can do these tests immediately themselves, actions can be taken faster in order to control hospital infections.

One of the aims of VALUE-Dx is to demonstrate the value of diagnostics to change the antibiotics prescribing behaviour. Can you comment on this?

During the COVID-19 pandemic, we used syndrome-based molecular tests to quickly diagnose intensive care patients and determine whether COVID is the cause of their deteriorating lung function or a superinfection, for example. The use of diagnostics definitely contributed to controlling antibiotic prescribing during this time. Running molecular tests can be very helpful for ICU physicians who oftentimes have to make quick decisions.

In regards to AMR, what’s the current situation in your country?

In Hungary, there are a lot of cases of multidrug-resistant bacteria called Acinetobacter. Luckily in Pécs, the situation is under control, on average we only have about 10 to 12 cases per year. Due to the Ukrainian refugees, there is also a rising problem of carbapenem-resistant Klebsiella in the East of the country which is slowly spreading to the centre of Hungary. These are not the only resistance issues we face, so there is a strong need to further take serious infection control measures, and other actions, i.e. broadening the use of antimicrobial stewardship.

Are there any antibiotic resistance awareness campaigns towards the general public?

Only during the World Antibiotic Awareness Week in November each year, but besides that no. There is still a lot of work to be done when it comes to educating the general public. However, another important factor is convincing insurance companies and national bodies to provide financing for diagnostic testing. In most cases, these tests cost more than running the actual antibiotic course. Governments should promote the use of point-of-care tests, which are available and quick, and benefit the antibiotic prescribing rates. If diagnostics can be done more accurately, this will also have a positive effect on the stay of patients in the ICU. Hospital management should become more aware of this.  

Agnes Sonnevend MD, PhD is an associate professor and consultant clinical microbiologist at the Department of Medical Microbiology and Immunology, Pecs University Medical School. She is the Head of Laboratory of Diagnostic Microbiology and Hospital Hygiene. Dr. Sonnevend’s main research areas are the molecular epidemiology of various multi-drug resistant organisms, the emergence and spread of such organisms, with special focus on plasmid and transposon mediated horizontal gene transfer of resistant determinants in Gram-negative bacteria, e.g. Enterobacterales, Acinetobacter baumannii and other non-fermenters isolated from clinical samples as well as from the environment and livestock.

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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.

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Interview with Professor Bojana Beović

Interview with Professor Bojana Beović

Read our interview with Professor Bojana Beović from the Ljubljana University Medical Centre. She elaborates on her role in the antimicrobial resistance (AMR) field, the impact of the COVID-19 pandemic on AMR and its research.

1. What is your role in the AMR field and what does it entail?

I am the Chair of the Antimicrobial Stewardship Unit at the Department of Infectious Diseases at the Ljubljana University Medical Centre. In addition, I am the chair of the so-called Intersectoral Coordination Mechanism for the Control of Antimicrobial Resistance at the Ministry of Health of Slovenia. This is a multidisciplinary group that manages AMR activities in the country. It includes the medical sector, the veterinary sector, and environmental specialists.

2. Why should people be concerned about AMR?

It is a well-known fact that antimicrobial resistance reduces the quality of care. Also in Europe, several analyses showed that AMR places a considerable burden on the healthcare system, including excessive mortality. Especially during epidemics, there was less attention paid to antimicrobial resistance and the conditions in many hospitals did not allow for its control, leading to a sharp increase. We will have to compensate for the loss caused by the COVID-19 pandemic in the coming years. In addition, the attention of the general population and media shifted from AMR to the Coronavirus disease, despite our efforts during the World Antibiotic Awareness Week last November.

3. What is the expected impact of the work you’re doing?

I have been working in this field for more than 20 years, and we were able to stabilise antimicrobial use and antimicrobial resistance through various activities. This does not mean that our job is done. I believe that stable daily activities are necessary in order to get the situation under control in a long term perspective. Therefore, in my opinion, the most important achievement is that antimicrobial stewardship is recognised and accepted as one of the normal daily activities in the hospital.

4. With regards to AMR, what’s the context in your country?

Eurobarometer data show that awareness of general public has decreased. In 2019, the Slovenian Government adopted a strategy for combating antimicrobial resistance, but because of the pandemic, many activities were not undertaken. The problem is that fighting AMR is a political commitment that is not followed by any funding. In Slovenia, most activities are still voluntary or financed from other sources and there is no financial support for the programmes of the government or the Minister of Health.

5. How did the COVID-19 pandemic impact the research on AMR?

It was obviously very difficult to cover the shifts during the pandemic with sufficient staff. Most of the doctors and microbiologists were involved in various COVID-19 activities. However, we were able to carry out two analyses. First, we sent out a survey asking doctors on an international scale whether they prescribed antibiotics to patients with COVID-19. The response from my colleagues in Slovenia showed relatively modest use. In addition, we conducted an international point prevalence study, comparing antibiotic use in COVID-19 patients in the ICU and in ordinary wards in Serbia, Croatia, Slovenia, and Italy. Our results showed that antibiotic use in Slovenia was relatively modest compared to other countries. We do not have data on antimicrobial resistance yet, but we are aware of a number of extremely resistant bacteria that were previously absent from some intensive care units in Slovenia, despite a generally relatively modest use of antibiotics. It is probably a consequence of antibiotic use and poor infection control during the most intensive peaks of the pandemic. 

Prof Bojana Beović, MD, PhD has been employed at the Department of Infectious Diseases at the University Medical Centre in Ljubljana since 1986. Since 2008 she is the head of the Antibiotic Committee in UMC Ljubljana. At the European Society of Clinical Microbiology and Infectious diseases (ESCMID), she was the honorary secretary of the ESCMID Study Group for Antibiotic stewardship (ESGAP) from 2009 to 2014. At the moment, she is the head of the ID Consultancy Service, chairs the Medical Chamber of Slovenia and is full professor of infectious diseases at the Medical School, University of Ljubljana. Her current focus of interest in research is antibiotic stewardship, and antibiotic therapy.

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