Research Article

Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection

Volume: 5 Number: 1 June 8, 2026
Bünyamin Kasap *, Arif Aksu
EN

Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection

Abstract

Objective: This study aimed to evaluate the results of multiplex real-time polymerase chain reaction (RT-PCR) respiratory panel tests, which play a critical role in the early and accurate diagnosis of acute respiratory tract infections, and to determine the distribution of detected pathogens according to age groups, referring clinical care settings, monthly, and seasonal variations. Material and Methods: This retrospective study evaluated the results of multiplex RT-PCR analyses performed on nasopharyngeal swab samples obtained from patients of all age groups who presented to Kanuni Training and Research Hospital for suspected respiratory tract infection between January 1, 2024, and December 31, 2025. The distribution of detected pathogens, co-infection patterns, and variations according to month, season, age, and clinical care setting of presentation were assessed using descriptive statistical methods. Results: At least one respiratory pathogen was detected in 60.6% (2441/4030) of nasopharyngeal samples, with viruses (86.7%) accounting for the majority of identified agents. Rhinovirus was the most frequently detected pathogen (17.9%), followed by adenovirus (9.6%), RSV A/B (7.9%), SARS-CoV-2 (6.7%), S. pyogenes (6.6%), and INF-A (6.3%). Co-infections were identified in 20.2% of positive samples, predominantly among children under 5 years of age. Rhinovirus occupied a central position within co-infection networks and was most frequently observed in association with adenovirus and RSV A/B. Conclusion: The study findings indicate that the distribution of respiratory pathogens detected in patients evaluated for suspected respiratory tract infection varied according to age, season, and clinical admission setting, thereby contributing to local epidemiological data.

Keywords

Multiplex RT-PCR, Respiratory tract infection, Virus

Supporting Institution

No financial support was received for this research.

Ethical Statement

Ethical approval for this study was obtained from the Scientific Research Ethics Committee of Trabzon Faculty of Medicine (Approval No: 2026/26004; Date: 05.01.2026).

Thanks

The authors would like to express their sincere gratitude to Dr. Zeliha AYDIN KASAP, Assistant Professor, for her valuable support and contribution to the statistical analyses of this study.

References

  1. Akçalı, S., Yılmaz, N., Güler, Özlem, Şanlidağ, T., & Anıl, M. (2020). Frequency of respiratory viruses in children with lower respiratory tract infection. Turkish Archives of Pediatrics, 48(3), 215–220. https://doi.org/10.4274/tpa.493
  2. Akçay, N., Tosun, D., Bingöl, İ., Bingöl, İ., Çıtak, A., Bayraktar, S., Menentoğlu, M. E., Şevketoğlu, E., Talip, M., Umman Serin, N., Bilgül, C., Koçoğlu Barlas, Ü., Telhan, L., Şahin, E., İnceköy Girgin, F., Kılınç, M. A., Bursal, B., & Baydemir, C. (2025). Severe pertussis infections in pediatric intensive care units: a multicenter study. European journal of pediatrics, 184(2), 138. https://doi.org/10.1007/s00431-025-05978-0
  3. Alp, A., Taşçı, O., Ergin, A., & Köseoğlu Eser, Ö. (2022). COVID-19 pandemisi öncesi ve sonrasında solunum yolu virüs paneli PCR test sonuçlarının değerlendirilmesi [Evaluation of the respiratory viral panel PCR test results before and after COVID-19 pandemic]. Mikrobiyoloji Bülteni, 56(4), 667–681. https://doi.org/10.5578/mb.20229605
  4. Arslan, A., Çiçek, C., Saz, E. U., Gülen, F., & Karakuş, H. S. (2016). Viral solunum yolu enfeksiyonlarının tanısında bir multipleks PCR yönteminin performansının değerlendirilmesi [Evaluation of the performance of a multiplex PCR method for the diagnosis of viral respiratory tract infections]. Türk Mikrobiyoloji Cemiyeti Dergisi, 46(4), 159–164. https://doi.org/10.5222/tmcd.2016.159
  5. Aydın, N. N., Karasahin, O., Aydın, M., Kerget, F., & İba Yılmaz, S. (2022). Yetişkinlerde COVID-19 öncesi solunum yolu viral etkenlerin epidemiyolojisi ve mevsimsel dağılımı [Epidemiology and seasonal distribution of respiratory viral agents before COVID-19 in adults]. Kırıkkale Üniversitesi Tıp Fakültesi Dergisi, 24(3), 496–500. https://doi.org/10.24938/kutfd.1112554
  6. Babawale, P. I., & Guerrero-Plata, A. (2024). Respiratory viral coinfections: Insights into epidemiology, immune response, pathology, and clinical outcomes. Pathogens, 13(4), Article 316. https://doi.org/10.3390/pathogens13040316
  7. Bartlow, A. W., Stromberg, Z. R., Gleasner, C. D., Hu, B., Davenport, K. W., Jakhar, S., Li, P. E., Vosburg, M., Garimella, M., Chain, P. S. G., Erkkila, T. H., Fair, J. M., & Mukundan, H. (2022). Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS global public health, 2(7), e0000811. https://doi.org/10.1371/journal.pgph.0000811
  8. Bukavaz, S., Gungor, K., Köle, M., & Ekuklu, G. (2025). Acute Respiratory Viral Infections Among Adult Patients in Edirne, Turkey. Tropical medicine and infectious disease, 10(2), 58. https://doi.org/10.3390/tropicalmed10020058
  9. Campbell, H., Gupta, S., Dolan, G. P., Kapadia, S. J., Kumar Singh, A., Andrews, N., & Amirthalingam, G. (2018). Review of vaccination in pregnancy to prevent pertussis in early infancy. Journal of medical microbiology, 67(10), 1426–1456. https://doi.org/10.1099/jmm.0.000829
  10. Chiu, Y. T., Tien, N., Lin, H. C., Wei, H. M., Lai, H. C., Chen, J. A., Low, Y. Y., Lin, H. H., Hsu, Y. L., & Hwang, K. P. (2022). Detection of respiratory pathogens by application of multiplex PCR panel during early period of COVID-19 pandemic in a tertiary hospital in Central Taiwan. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi, 55(6 Pt 2), 1144–1150. https://doi.org/10.1016/j.jmii.2021.09.011
APA
Kasap, B., & Aksu, A. (2026). Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection. Farabi Medical Journal, 5(1), 1-16. https://doi.org/10.59518/farabimedj.1934767
AMA
1.Kasap B, Aksu A. Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection. Farabi Medical Journal. 2026;5(1):1-16. doi:10.59518/farabimedj.1934767
Chicago
Kasap, Bünyamin, and Arif Aksu. 2026. “Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients With Suspected Respiratory Tract Infection”. Farabi Medical Journal 5 (1): 1-16. https://doi.org/10.59518/farabimedj.1934767.
EndNote
Kasap B, Aksu A (June 1, 2026) Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection. Farabi Medical Journal 5 1 1–16.
IEEE
[1]B. Kasap and A. Aksu, “Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection”, Farabi Medical Journal, vol. 5, no. 1, pp. 1–16, June 2026, doi: 10.59518/farabimedj.1934767.
ISNAD
Kasap, Bünyamin - Aksu, Arif. “Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients With Suspected Respiratory Tract Infection”. Farabi Medical Journal 5/1 (June 1, 2026): 1-16. https://doi.org/10.59518/farabimedj.1934767.
JAMA
1.Kasap B, Aksu A. Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection. Farabi Medical Journal. 2026;5:1–16.
MLA
Kasap, Bünyamin, and Arif Aksu. “Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients With Suspected Respiratory Tract Infection”. Farabi Medical Journal, vol. 5, no. 1, June 2026, pp. 1-16, doi:10.59518/farabimedj.1934767.
Vancouver
1.Bünyamin Kasap, Arif Aksu. Molecular Epidemiology of Respiratory Pathogens Identified by Multiplex PCR in Patients with Suspected Respiratory Tract Infection. Farabi Medical Journal. 2026 Jun. 1;5(1):1-16. doi:10.59518/farabimedj.1934767