Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection

Yasemin Dostuoğlu; Murat Karameşe

Araştırma Makalesi

Yıl 2025, Cilt: 15 Sayı: 1, 58 - 63, 30.04.2025

Yasemin Dostuoğlu Murat Karameşe

Öz

Kaynakça

1. Quinn-Bohmann N, Freixas-Coutin JA, Seo J, Simmons R, Diener C, Gibbons SM. Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC Biol. 2024;22:1–14.
2. Girgin HC. Çocuk hastalıkları servisine solunum yolu enfeksiyonu ile yatan hastalarda solunum virüs epidemiyolojisi ve klinik özellikleri [Doktora Tezi]. Dokuz Eylül Üniversitesi;İzmir, Türkiye, 2022.
3. Ma L, Zhu H, Jiang Y, Kong X, Gao P, Liu Y, et al. Development of a novel multiplex PCR method for the rapid detection of SARS-CoV-2, influenza A virus, and influenza B virus. Int J Anal Chem. 2024:4950391.
4. Thomas M, Bomar PA. Upper Respiratory Tract Infection. StatPearls. Treasure Island (FL). 2024.
5. Büyükşahin HN, Özçelik U. Acute bronchiolitis. Ankara EAH Tıp Derg. 2022;54(3):479–486.
6. Yildiz GN, Tukenmez G, Topaloglu I, Celebi O, Karamese M. Retrospective Evaluation of the Frequency of Respiratory Pathogens in Patients Admitted to Kafkas University Medical Faculty Hospital. Dicle Med J. 2024;51(4):539–546.
7. Parrott GL, Kinjo T, Fujita J. A compendium for Mycoplasma pneumoniae. Front Microbiol. 2016;7:513.
8. Dion CF, Ashurst JV. Streptococcus pneumoniae. StatPearls. Treasure Island (FL). 2024.
9. Dereköy S, Güçlü O. Upper respiratory tract infections. Klinik Tıp Aile Hekimliği. 2016;8(4):33–43.
10. Young JH, Jung BK, Kim JK. Epidemiological characterization of respiratory pathogens using the multiplex PCR FilmArray™ Respiratory Panel. Diagnostics. 2024;14(7):734.
11. Yuksel H, Turkel A. New Viral Pathogens among Pediatric Patients with Pneumonia. Güncel Göğüs Hastalıkları Serisi. 2014;2(1):106–116.
12. Man WH, de Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259–70.
13. Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, et al. Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2. Sci Rep. 2023;13(1):16867.
14. Kuşkucu MA, Mete B, Tabak F, Midilli K. Prevalence and Seasonal Distribution of Respiratory Viruses in Adults Between 2010–2018. Turk Mikrobiyol Cem Derg. 2020;50(1):21–6.
15. Essaidi-Laziosi M, Alvarez C, Puhach O, Sattonnet-Roche P, Torriani G, Tapparel C, et al. Sequential infections with rhinovirus and influenza modulate the replicative capacity of SARS-CoV-2 in the upper respiratory tract. Emerging Microbes Infect. 2022;11(1):413–24.
16. Mifsud EJ, Kuba M, Barr IG. Innate immune responses to influenza virus infections in the upper respiratory tract. Viruses.2021;13(10):2090.
17. Bell J, Chua A, Eccles R, Salvi S, Schellack N, Wang DY. Early intervention in acute upper respiratory tract infections. S Afr Pharm J. 2022;89(5):30–3.
18. Şahin MC. Investıgatıon of the Prevalence of Viral and Bacterial Agents by Multiplex PCR Method in Patients with a Pre-Diagnosis of Acute Respiratory Tract Infection in Isparta Province. Med J SDU. 2022;29(2):171–8.
19. Talay MN, Özer E. Investigation of Pathogen Distribution by Direct and Indirect Immunofluorescence Microscopy in Patients followed up with a Pre-Diagnosis of Atypical Pneumonia in a Pediatric Intensive Care Unit. Dicle Med J. 2022;49(3):513–20.
20. Aydın NN, Köse O, Aydın M, Kerget F, İba Yılmaz S. Epidemiology and Seasonal Distribution of Respiatory Viral Agents in the Pre-COVID-19 Period in Adults. Kırıkkale Üniv Tıp Fak Derg. 2022;24(3):496–500.
21. Kwiyolecha E, Groendahl B, Okamo B, Kayange N, Manyama F, Kidenya BR, et al. Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania. Sci Rep. 2020;10(1):18490.
22. Li ZJ, Zhang HY, Ren LL, Lu QB, Ren X, Zhang CH, et al. Etiological and epidemiological features of acute respiratory infections in China. Nat Commun. 2021;12(1):5026.
23. Wang H, Li X, Zheng Y, Verhagen LM, Gu J, Li L, et al. Concordance in pathogen identification at the upper and lower respiratory tract of children with severe pneumonia. BMC Infect Dis. 2023;23:1–8.
24. Aydın E, Güney Yılmaz G, Aydın N, Dicle Y, Renders DP. Distribution of Respiratory Pathogens After the COVID-19 Pandemic: A Single-Center Pediatric Study From Türkiye. Kafkas J Med Sci. 2023;13(3):321–328.
25. Tekinsoy M. Çocukluk çağında üst solunum yolu enfeksiyonu etkeni virüslerin retrospektif olarak araştırılması [Uzmanlık Tezi]. Bursa Uludağ Üniversitesi;Bursa, Türkiye, 2022.
26. Karabulut N, Alacam S, Sen E, Karabey M, Yakut N. The epidemiological features and pathogen spectrum of respiratory tract infections, Istanbul, Turkiye, from 2021 to 2023. Diagnostics. 2024;14(11).
27. Bell C, Goss M, Norton D, Barlow S, Temte E, He C, et al. Descriptive epidemiology of pathogens associated with acute respiratory infection in a community-based study of K-12 school children (2015–2023). Pathogens. 2024;13(4).
28. Nieto-Rivera B, Saldana-Ahuactzi Z, Parra-Ortega I, Flores- Alanis A, Carbajal-Franco E, Cruz-Rangel A, et al. Frequency of respiratory virus-associated infection among children and adolescents from a tertiary-care hospital in Mexico City. Sci Rep. 2023;13(1):19763.
29. Manna S, McAuley J, Jacobson J, Nguyen CD, Ullah MA, Sebina I, et al. Synergism and antagonism of bacterial-viral coinfection in the upper respiratory tract. mSphere. 2022;7(1):e0098421.
30. Nickbakhsh S, Mair C, Matthews L, Reeve R, Johnson PCD, Thorburn F, et al. Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A. 2019;116(52):27142–50.

Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection

Yıl 2025, Cilt: 15 Sayı: 1, 58 - 63, 30.04.2025

Yasemin Dostuoğlu Murat Karameşe

Öz

Aim: Upper respiratory tract infection (URTI) complaints are the most common causes of admission to outpatient clinics and rapid detection by Multiplex-PCR method contributes to the monitoring and control of infection by easily evaluating the etiology of viral and bacterial agents regionally. The aim of this study was to evaluate the etiology of pathogens with a 24-X viral and bacterial respiratory Multiplex-PCR panel in patients who admitted to XXX University XXX Hospital with URTI symptoms between November 2023 and February 2024.
Materials and Methods: The presence of viral and bacterial pathogens was analyzed by Multiplex-PCR method in nasopharyngeal swab samples obtained from 100 patients diagnosed with URTI by physical examination such as allergic rhinitis and acute bronchitis. The respiratory panel was containing 24 different microorganism such as SARS CoV-2, Influenza-A/B, Human Rhinovirus/Enterovirus, Human Metapneumovirus, Respiratory Syncytial Virus A/B, Human Parainfluenza Virus-1/2/3/4, Human Coronavirus 229E/OC43/NL63/HKU1, Human Parechovirus, Adenovirus, Human Bocavirus, Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila and Bordotella pertussis.
Results: According to the findings, the highest number of applications was in January. Out of 100 patients, 73% (n=73) were positive and 27% (n=27) were negative, the most common viral agent was INF A (n=33, 26.9%) while the most common bacterial agent was S.pneumoniae (n=19, 15.4%). Of 73 positive patients, 38.3% (n=28) had co-infection, 11% (n=8) had only bacterial agents and 50.7% (n=37) had viral agents.
Conclusions: In conclusion, URTI agents were rapidly detected by Multiplex-PCR and their incidence was investigated in this study. Finally, it is aimed to prevent possible epidemics, unnecessary antibiotic use, mortality and morbidity, and to contribute to other academic studies with rapid diagnosis and treatment of URTI infections.

Anahtar Kelimeler

URTI, SARS-CoV-2, Influenza, Multiplex PCR

Kaynakça

1. Quinn-Bohmann N, Freixas-Coutin JA, Seo J, Simmons R, Diener C, Gibbons SM. Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC Biol. 2024;22:1–14.
2. Girgin HC. Çocuk hastalıkları servisine solunum yolu enfeksiyonu ile yatan hastalarda solunum virüs epidemiyolojisi ve klinik özellikleri [Doktora Tezi]. Dokuz Eylül Üniversitesi;İzmir, Türkiye, 2022.
3. Ma L, Zhu H, Jiang Y, Kong X, Gao P, Liu Y, et al. Development of a novel multiplex PCR method for the rapid detection of SARS-CoV-2, influenza A virus, and influenza B virus. Int J Anal Chem. 2024:4950391.
4. Thomas M, Bomar PA. Upper Respiratory Tract Infection. StatPearls. Treasure Island (FL). 2024.
5. Büyükşahin HN, Özçelik U. Acute bronchiolitis. Ankara EAH Tıp Derg. 2022;54(3):479–486.
6. Yildiz GN, Tukenmez G, Topaloglu I, Celebi O, Karamese M. Retrospective Evaluation of the Frequency of Respiratory Pathogens in Patients Admitted to Kafkas University Medical Faculty Hospital. Dicle Med J. 2024;51(4):539–546.
7. Parrott GL, Kinjo T, Fujita J. A compendium for Mycoplasma pneumoniae. Front Microbiol. 2016;7:513.
8. Dion CF, Ashurst JV. Streptococcus pneumoniae. StatPearls. Treasure Island (FL). 2024.
9. Dereköy S, Güçlü O. Upper respiratory tract infections. Klinik Tıp Aile Hekimliği. 2016;8(4):33–43.
10. Young JH, Jung BK, Kim JK. Epidemiological characterization of respiratory pathogens using the multiplex PCR FilmArray™ Respiratory Panel. Diagnostics. 2024;14(7):734.
11. Yuksel H, Turkel A. New Viral Pathogens among Pediatric Patients with Pneumonia. Güncel Göğüs Hastalıkları Serisi. 2014;2(1):106–116.
12. Man WH, de Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259–70.
13. Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, et al. Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2. Sci Rep. 2023;13(1):16867.
14. Kuşkucu MA, Mete B, Tabak F, Midilli K. Prevalence and Seasonal Distribution of Respiratory Viruses in Adults Between 2010–2018. Turk Mikrobiyol Cem Derg. 2020;50(1):21–6.
15. Essaidi-Laziosi M, Alvarez C, Puhach O, Sattonnet-Roche P, Torriani G, Tapparel C, et al. Sequential infections with rhinovirus and influenza modulate the replicative capacity of SARS-CoV-2 in the upper respiratory tract. Emerging Microbes Infect. 2022;11(1):413–24.
16. Mifsud EJ, Kuba M, Barr IG. Innate immune responses to influenza virus infections in the upper respiratory tract. Viruses.2021;13(10):2090.
17. Bell J, Chua A, Eccles R, Salvi S, Schellack N, Wang DY. Early intervention in acute upper respiratory tract infections. S Afr Pharm J. 2022;89(5):30–3.
18. Şahin MC. Investıgatıon of the Prevalence of Viral and Bacterial Agents by Multiplex PCR Method in Patients with a Pre-Diagnosis of Acute Respiratory Tract Infection in Isparta Province. Med J SDU. 2022;29(2):171–8.
19. Talay MN, Özer E. Investigation of Pathogen Distribution by Direct and Indirect Immunofluorescence Microscopy in Patients followed up with a Pre-Diagnosis of Atypical Pneumonia in a Pediatric Intensive Care Unit. Dicle Med J. 2022;49(3):513–20.
20. Aydın NN, Köse O, Aydın M, Kerget F, İba Yılmaz S. Epidemiology and Seasonal Distribution of Respiatory Viral Agents in the Pre-COVID-19 Period in Adults. Kırıkkale Üniv Tıp Fak Derg. 2022;24(3):496–500.
21. Kwiyolecha E, Groendahl B, Okamo B, Kayange N, Manyama F, Kidenya BR, et al. Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania. Sci Rep. 2020;10(1):18490.
22. Li ZJ, Zhang HY, Ren LL, Lu QB, Ren X, Zhang CH, et al. Etiological and epidemiological features of acute respiratory infections in China. Nat Commun. 2021;12(1):5026.
23. Wang H, Li X, Zheng Y, Verhagen LM, Gu J, Li L, et al. Concordance in pathogen identification at the upper and lower respiratory tract of children with severe pneumonia. BMC Infect Dis. 2023;23:1–8.
24. Aydın E, Güney Yılmaz G, Aydın N, Dicle Y, Renders DP. Distribution of Respiratory Pathogens After the COVID-19 Pandemic: A Single-Center Pediatric Study From Türkiye. Kafkas J Med Sci. 2023;13(3):321–328.
25. Tekinsoy M. Çocukluk çağında üst solunum yolu enfeksiyonu etkeni virüslerin retrospektif olarak araştırılması [Uzmanlık Tezi]. Bursa Uludağ Üniversitesi;Bursa, Türkiye, 2022.
26. Karabulut N, Alacam S, Sen E, Karabey M, Yakut N. The epidemiological features and pathogen spectrum of respiratory tract infections, Istanbul, Turkiye, from 2021 to 2023. Diagnostics. 2024;14(11).
27. Bell C, Goss M, Norton D, Barlow S, Temte E, He C, et al. Descriptive epidemiology of pathogens associated with acute respiratory infection in a community-based study of K-12 school children (2015–2023). Pathogens. 2024;13(4).
28. Nieto-Rivera B, Saldana-Ahuactzi Z, Parra-Ortega I, Flores- Alanis A, Carbajal-Franco E, Cruz-Rangel A, et al. Frequency of respiratory virus-associated infection among children and adolescents from a tertiary-care hospital in Mexico City. Sci Rep. 2023;13(1):19763.
29. Manna S, McAuley J, Jacobson J, Nguyen CD, Ullah MA, Sebina I, et al. Synergism and antagonism of bacterial-viral coinfection in the upper respiratory tract. mSphere. 2022;7(1):e0098421.
30. Nickbakhsh S, Mair C, Matthews L, Reeve R, Johnson PCD, Thorburn F, et al. Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A. 2019;116(52):27142–50.

Toplam 30 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	İngilizce
Konular	Klinik Mikrobiyoloji
Bölüm	Araştırma Makalesi
Yazarlar	Yasemin Dostuoğlu Murat Karameşe
Yayımlanma Tarihi	30 Nisan 2025
Gönderilme Tarihi	21 Aralık 2024
Kabul Tarihi	29 Ocak 2025
Yayımlandığı Sayı	Yıl 2025 Cilt: 15 Sayı: 1

Kaynak Göster

APA	Dostuoğlu, Y., & Karameşe, M. (2025). Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection. Kafkas Journal of Medical Sciences, 15(1), 58-63.
AMA	Dostuoğlu Y, Karameşe M. Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection. KAFKAS TIP BİL DERG. Nisan 2025;15(1):58-63.
Chicago	Dostuoğlu, Yasemin, ve Murat Karameşe. “Investigation of Viral and Bacterial Agents in Samples Taken from Patients With Suspected Upper Respiratory Tract Infection”. Kafkas Journal of Medical Sciences 15, sy. 1 (Nisan 2025): 58-63.
EndNote	Dostuoğlu Y, Karameşe M (01 Nisan 2025) Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection. Kafkas Journal of Medical Sciences 15 1 58–63.
IEEE	Y. Dostuoğlu ve M. Karameşe, “Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection”, KAFKAS TIP BİL DERG, c. 15, sy. 1, ss. 58–63, 2025.
ISNAD	Dostuoğlu, Yasemin - Karameşe, Murat. “Investigation of Viral and Bacterial Agents in Samples Taken from Patients With Suspected Upper Respiratory Tract Infection”. Kafkas Journal of Medical Sciences 15/1 (Nisan 2025), 58-63.
JAMA	Dostuoğlu Y, Karameşe M. Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection. KAFKAS TIP BİL DERG. 2025;15:58–63.
MLA	Dostuoğlu, Yasemin ve Murat Karameşe. “Investigation of Viral and Bacterial Agents in Samples Taken from Patients With Suspected Upper Respiratory Tract Infection”. Kafkas Journal of Medical Sciences, c. 15, sy. 1, 2025, ss. 58-63.
Vancouver	Dostuoğlu Y, Karameşe M. Investigation of Viral and Bacterial Agents in Samples Taken from Patients with Suspected Upper Respiratory Tract Infection. KAFKAS TIP BİL DERG. 2025;15(1):58-63.

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