Antibiotics | Interview with One of the Authors—Dr. Elshafia Ali Hamid Mohammed

Name: Dr. Elshafia Ali Hamid Mohammed
Affiliation: University of Debrecen, Hungary

“Antibiotic Resistance in Aquaculture: Challenges, Trends Analysis, and Alternative Approaches”
by Elshafia Ali Hamid Mohammed, Béla Kovács, Ronald Kuunya, Eltayeb Omaima Awad Mustafa, Azza Siddig Hussien Abbo and Károly Pál
Antibiotics 2025, 14(6), 598; https://doi.org/10.3390/antibiotics14060598

The following is an interview with Dr. Elshafia Ali Hamid Mohammed:

1. First of all, thank you for taking the time to speak with us, and congratulations on publishing your highly cited paper in Antibiotics. To begin, could you briefly introduce yourself and tell us about your current research focus?
Thank you very much for having me. My name is Elshafia Ali Hamid Mohammed. It is a pleasure to be invited for this interview. I am a Sudanese researcher at Agricultural Research Corporation-Sudan, currently a PhD candidate at the University of Debrecen, Hungary. My current research focuses on investigating antimicrobial resistance in the aquatic environment, aquatic microbiology, probiotics, and fish health. So, at the beginning of my PhD research, we investigated antimicrobial resistance in Hungarian fish farms to know what types of resistant bacteria exist and to try to understand the resistance mechanisms. My goal was to publish our first article in a reputable, high-impact journal that would reach the appropriate scientific audience.
After exploring several options, I chose Antibiotics, which is a highly ranked journal in the fields of pharmacology and toxicology (among the top 10% journals in this field). The journal closely matched my research interests, making it the ideal choice for our work.
Our first paper in Antibiotics focused on the use of beneficial microorganisms, particularly probiotics, as a sustainable alternative to antibiotics in aquaculture. The response from the scientific community exceeded our expectations. Within the first year after publication, our article was cited by more than 70 scientific publications and received over 17,000 reads. The most rewarding aspect was not simply the numbers but knowing that researchers around the world were building on our findings. That gave me confidence that our work is making a meaningful contribution to the field.

2. What was your experience like publishing in Antibiotics?
When I was reading papers on antimicrobial resistance in aquaculture, I noticed that many of the studies I found most relevant and useful had been published in Antibiotics. That caught my attention because it showed me that the journal was publishing high-quality research in exact areas I was working on. As I continued following the journal, I became more familiar with its scope, the quality of its publications, and its visibility within the research community. When it came time to choose a journal for our first manuscript, Antibiotics was one of my first choices. I felt that the journal was a good scientific fit for my work and that it would reach the audience most interested in antimicrobial resistance and sustainable alternatives to antibiotics. Looking back, I believe it was the right decision. Publishing in Antibiotics allowed our 3 papers that have been published in 2025 to reach a broad international audience with more than 35000 reads and 158 citations. It has been very rewarding to see other researchers read and cite our work.
From submission to publication, the editorial process was smooth and well organized. Communication with the Editorial Office was always clear and timely, so I was consistently informed about the status of my manuscript.
I also greatly appreciated the reviewers’ comments. Their feedback was constructive and helped us improve the manuscript in several important ways, rather than simply identifying its weaknesses. They provided practical suggestions that strengthened the quality of our work. As a researcher, I believe this is exactly what a good peer-review process should achieve.
It was also very rewarding to see our paper receive such a positive response from the scientific community. The large number of citations and readers indicates that the topic addresses important scientific questions.

3. What inspired you to focus on antimicrobial resistance and aquatic microbiology?
My interest in this field comes from the global challenge of antimicrobial resistance and its impact on both animal and public health. Aquatic environments are unique because they serve as reservoirs where diverse microorganisms interact and where antimicrobial resistance genes can emerge, persist, and spread. Understanding these processes is essential for developing sustainable aquaculture practices.
What continues to motivate me is the complexity of these microbial ecosystems. Microorganisms interact not only with one another but also with environmental factors such as water quality, temperature, pH, and farm management practices. Investigating these interactions requires a multidisciplinary approach that combines microbiology, molecular biology, genetics, and environmental science.
Another fascinating aspect is that antimicrobial resistance is evolving. Bacteria can acquire and exchange resistance genes through mechanisms such as horizontal gene transfer caused by mobile genetic elements. This allows resistance to spread not only within a single bacterial species but also between different species and across different environments.

4. Looking ahead, what do you see as the next steps in your research?
I believe antimicrobial resistance will remain one of the most important research priorities in the coming years. Although significant progress has been made, many important questions remain unanswered. Antimicrobial resistance is a dynamic problem that affects not only fish but also the environment and human health. This is why the One Health approach has become increasingly important.
During my PhD research, we isolated a wide range of bacterial species from Hungarian fish farms and identified them using MALDI-TOF MS technology. These included, for example, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium. Some of these bacteria exhibited resistance to clinically important antibiotics, including vancomycin-resistant enterococci, highlighting their potential significance as reservoirs of antimicrobial resistance.
The next step in our research is to investigate the genetic basis of this resistance. We would like to identify the antimicrobial resistance genes carried by these bacteria and understand the molecular mechanisms responsible for their dissemination, particularly the role of horizontal gene transfer through mobile genetic elements such as plasmids. I hope to better understand how resistance genes circulate among aquatic environments, fish, and humans, providing valuable evidence to support One Health strategies for monitoring and controlling antimicrobial resistance.

5. Over the next few years, which research areas or emerging questions do you believe will become priorities in your field?
One area that deserves greater attention is understanding how bacteria acquire antimicrobial resistance. Because bacteria are remarkably adaptable, they can exchange resistance genes, allowing resistance to spread rapidly within microbial communities. Understanding how this process occurs under different environmental conditions is essential for developing effective strategies to limit the spread of resistance.
Another exciting direction is the integration of metagenomics into antimicrobial resistance research. These technologies allow us to investigate entire microbial communities instead of focusing only on individual bacterial isolates, providing a much more comprehensive understanding of environmental resistomes and the pathways through which resistance genes circulate.
I also expect growing interest in sustainable alternatives to antibiotics, including probiotics, prebiotics, postbiotics, and improved disease management strategies, particularly in aquaculture and livestock production.

6. What is your perspective on open access publishing?
As researchers, we invest significant time and effort into conducting experiments, collecting and analyzing data, interpreting results, and writing manuscripts. It is therefore very important that the outcomes of our findings are accessible to as many people as possible, not only researchers at well-funded institutions, but also scientists, students, and policymakers around the world.
This is especially important in fields such as antimicrobial resistance, where research findings can have direct practical applications. For example, if someone is working to improve disease management in aquaculture or developing strategies to reduce antibiotic use, having immediate access to the latest scientific evidence can make a real difference.
For me, coming from Sudan and now conducting research in Hungary, I have experienced different research environments. I know that access to subscription-based journals can be challenging, particularly in developing countries. So, open access helps reduce these barriers and provides researchers with more equal opportunities to access scientific knowledge.
Of course, one challenge for authors is the article processing charge (APC), which can be difficult to afford, especially for researchers with limited funding. While open access greatly benefits readers, reducing publication costs remains an important consideration for many authors.

7. You also serve as a reviewer for several journals. How would you describe your experience with the peer-review process?
I serve as a reviewer for several journals, including Elsevier journals, MDPI journals, and Frontiers in Microbiology. Reviewing manuscripts has given me a different perspective on scientific publishing. It has made me realize how much responsibility reviewers have in ensuring that research is accurate, well presented, and scientifically sound. At the same time, it has also helped me become a better author because I now understand what reviewers are looking for when they evaluate a manuscript.
When I receive an invitation to review a manuscript, I first read it carefully and appreciate the effort the authors have invested in their research. My goal is to provide a fair review that not only identifies a list of weaknesses but also offers practical suggestions to enhance the scientific quality and readability of the manuscript.
I believe peer review should help authors improve their work, and I enjoy contributing to that process. I continue to receive regular invitations to review manuscripts for Animals MDPI, which I see as a positive indication that my reviews are valued.

8. Finally, what advice would you give to young researchers who are just beginning their careers?
My advice is simple: read extensively in your field.
Reading scientific literature helps you identify research gaps, understand current challenges, and develop a clear research plan. Every meaningful scientific contribution begins with a solid understanding of existing knowledge. At this point, I would also like to express my thanks to Prof. Komlósi István and my supervisor, Dr. Károly Pál, as this was one of the first pieces of advice they gave me when I started my PhD journey at the University of Debrecen. Their advice on the importance of continuous reading has guided me throughout my research.