cover_issue_7_en_US-1-1

Volume 1, Issue 4 (July 2022)

Authors' Guidelines
PDF
Make a Submission
Other Format
Conventional PCR versus Culture Method to Detect Common Fungal Pathogens in Patients with Respiratory Diseases
Hadeel Jamal Rashied
 Department of Teaching Laboratory,AL-Emamain AL-Khadhymian Teaching Hospital,Baghdad - Iraq
 hadeeljamal654@gmail.com
 Corresponding Author
Azhar A. Al-Attraqchi
 Department of Microbiology/College of Medicine/ Al-Nahrain University, Baghdad – Iraq
Amar Kasim Muhmmed
 Department of Medicine Baghdad Teaching hospital, Medical City Baghdad – Iraq
ISSN(e): 2790-296X
ISSN(p): 2957-5826
About the Journal
Editor in Chief:
Prof. Dr. Emad Al-Mulla
 
Frequency:
BCS is published quarterly
 
Publisher:
 
Co-Publisher:
 
Editorial Office:
Commercial Plot 33 Millennium Plaza, G-15 Markaz, Margalla 02, Islamabad, Pakistan

The study aimed to assess the frequency of invasive fungal infection in patients with respiratory diseases by conventional and molecular methods. This study included 117 Broncho alveolar lavage (BAL) samples were collected from patients with respiratory disease (79 male and 38 female) with ages ranged between (20-80) years, who attended Medicine Baghdad Teaching hospital and AL-Emamain AL-Khadhymian Medical City, during the period from September 2019 to April 2020. The results in PCR versus culture methods in this study showed that out of 117 samples of fungal infections 30(25.6 %) were detected by culture method, while the 24(20.5%) samples were detected by PCR technique, the most commonly diagnosed pathogenic fungi is Candida spp. followed by Aspergillus spp. By considering the culture method as a gold standard against the PCR technique, the results show that the sensitivity and specificity of PCR were (86.6%) and (100%) respectively.

  1. Ahmed, M. M., Farghaly, A. A., Raafat, R. H., & Abd Elsattar, W. M. (2019). Study of the prevalence and pattern of fungal pneumonias in respiratory intensive care units. Egyptian Journal of Bronchology, 13(4), 545-550. https://doi.org/10.4103/ejb.ejb_37_19
  2. Akram, Z., Al-Kheraif, A. A., Kellesarian, S. V., Vohra, F., & Javed, F. (2018). Comparison of oral Candida carriage in waterpipe smokers, cigarette smokers, and non-smokers. Journal of Oral Science, 60(1), 115-120. https://doi.org/10.2334/josnusd.17-0090
  3. Aluyi, H. S. A., Otajevwo, F. D., & Iweriebor, O. (2010). Incidence of pulmonary mycoses in patients with acquired immunodeficiency diseases. Nigerian Journal of Clinical Practice, 13(1). https://www.ajol.info/index.php/njcp/article/view/53199
  4. Arvanitis, M., Anagnostou, T., Fuchs, B. B., Caliendo, A. M., & Mylonakis, E. (2014). Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clinical Microbiology Reviews, 27(3), 490-526. https://doi.org/10.1128/CMR.00091-13
  5. Baddley, J. W., Winthrop, K. L., Patkar, N. M., Delzell, E., Beukelman, T., Xie, F., ... & Curtis, J. R. (2011). Geographic distribution of endemic fungal infections among older persons, United States. Emerging infectious diseases, 17(9), 1664. https://doi.org/10.3201%2Feid1709.101987
  6. Badiee, P., Kordbacheh, P., Alborzi, A., Malekhoseini, S., Ramzi, M., Mirhendi, H., ... & Shakiba, E. (2009). Study on invasive fungal infections in immunocompromised patients to present a suitable early diagnostic procedure. International Journal of Infectious Diseases, 13(1), 97-102. https://doi.org/10.1016/j.ijid.2008.04.011
  7. Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P., & Kauserud, H. (2010). ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC microbiology, 10(1), 1-9. https://doi.org/10.1186/1471-2180-10-189
  8. Bezdicek, M., Lengerova, M., Ricna, D., Weinbergerova, B., Kocmanova, I., Volfova, P., ... & Racil, Z. (2016). Rapid detection of fungal pathogens in bronchoalveolar lavage samples using panfungal PCR combined with high resolution melting analysis. Medical Mycology, 54(7), 714-724. https://doi.org/10.1093/mmy/myw032
  9. Bulpa, P., Dive, A., & Sibille, Y. (2007). Invasive pulmonary aspergillosis in patients with chronic obstructive pulmonary disease. European Respiratory Journal, 30(4), 782-800. https://doi.org/10.1183/09031936.00062206
  10. Cao, A. M. Y., Choy, J. P., Mohanakrishnan, L. N., Bain, R. F., & van Driel, M. L. (2013). Chest radiographs for acute lower respiratory tract infections. The Cochrane Database of Systematic Reviews, 2013(12). https://doi.org/10.1002/14651858.CD009119.pub2
  11. Capoor, M. R., Puri, S., Raheja, H., Mohindra, R., Gupta, D. K., Verma, P. K., & Chowdhary, R. (2017). Screening of invasive fungal infections by a real-time panfungal (pan-ACF) polymerase chain reaction assay in patients with haematological malignancy. Indian Journal of Medical Microbiology, 35(1), 41-47. https://doi.org/10.4103/ijmm.IJMM_15_543
  12. Chadana, M., Oberoi, L., & Malhotra, A. (2019). Emerging Fungal Respiratory Tract Infections in a Tertiary Care Hospital of North India, Punjab. Journal of Medical Science and Clinical Research, 7(8), 841-844. http://216.10.240.19/v7-i8/143%20jmscr.pdf
  13. Ekenna, O., Uba, A., Chikwem, J. O., Mambula, S., Aliyu, M. B., & Mohammed, I. (2007). Relevance of moldy fungi as agents of chronic lower respiratory tract infection in patients seen in Maiduguri, Nigeria. West African journal of medicine, 26(2), 117-120. https://europepmc.org/article/med/17939312
  14. Fajarningsih, N. D. (2016). Internal Transcribed Spacer (ITS) as DNA barcoding to identify fungal species: a review. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology, 11(2), 37-44. https://doi.org/10.15578/squalen.v11i2.213
  15. Jahromi, S. B., & Khaksar, A. A. (2002). FUNGAL ISOLATES OF THE RESPIRATORY TRACT: 460. Critical Care Medicine, 30(12), A111.
  16. Jha, B. J., Dey, S., Tamang, M. D., Joshy, M. E., Shivananda, P. G., & Brahmadatan, K. N. (2006). Characterization of Candida species isolated from cases of lower respiratory tract infection. Kathmandu University medical journal (KUMJ), 4(3), 290-294. https://europepmc.org/article/med/18603921
  17. José, R. J., Periselneris, J. N., & Brown, J. S. (2020). Opportunistic bacterial, viral and fungal infections of the lung. Medicine, 48(6), 366-372. https://doi.org/10.1016/j.mpmed.2020.03.006
  18. Lao, M., Li, C., Li, J., Chen, D., Ding, M., & Gong, Y. (2020). Opportunistic invasive fungal disease in patients with type 2 diabetes mellitus from Southern China: clinical features and associated factors. Journal of Diabetes Investigation, 11(3), 731-744. https://doi.org/10.1111/jdi.13183
  19. Lass-Flörl, C., Mutschlechner, W., Aigner, M., Grif, K., Marth, C., Girschikofsky, M., ... & Nachbaur, D. (2013). Utility of PCR in diagnosis of invasive fungal infections: real-life data from a multicenter study. Journal of clinical microbiology, 51(3), 863-868. https://doi.org/10.1128/JCM.02965-12
  20. Lengerova, M., Racil, Z., Hrncirova, K., Kocmanova, I., Volfova, P., Ricna, D., ... & Mayer, J. (2014). Rapid detection and identification of mucormycetes in bronchoalveolar lavage samples from immunocompromised patients with pulmonary infiltrates by use of high-resolution melt analysis. Journal of Clinical Microbiology, 52(8), 2824-2828. https://doi.org/10.1128/JCM.00637-14
  21. Louisiana Office of Public Health – Infectious Disease Epidemiology Section – Annual Report. Cryptococcosis. 2010.
  22. Mandell, G. L., Douglas Jr, R. G., & Bennett, J. E. (1979). Principles and practice of infectious diseases. Volumes 1 and 2. John Wiley & Sons.
  23. Mikulska, M., Furfaro, E., De Carolis, E., Drago, E., Pulzato, I., Borghesi, M. L., ... & Viscoli, C. (2019). Use of Aspergillus fumigatus real-time PCR in bronchoalveolar lavage samples (BAL) for diagnosis of invasive aspergillosis, including azole-resistant cases, in high risk haematology patients: the need for a combined use with galactomannan. Medical mycology, 57(8), 987-996. https://doi.org/10.1093/mmy/myz002
  24. Njovu, I. K., Musinguzi, B., Mwesigye, J., Kassaza, K., Turigurwa, J., Nuwagira, E., ... & Itabangi, H. (2021). Status of pulmonary fungal pathogens among individuals with clinical features of pulmonary tuberculosis at Mbarara University Teaching Hospital in Southwestern Uganda. Therapeutic Advances in Infectious Disease, 8, 20499361211042477. https://doi.org/10.1177/20499361211042477
  25. Njovu, I. K., Musinguzi, B., Mwesigye, J., Kassaza, K., Turigurwa, J., Nuwagira, E., ... & Itabangi, H. (2021). Status of pulmonary fungal pathogens among individuals with clinical features of pulmonary tuberculosis at Mbarara University Teaching Hospital in Southwestern Uganda. Therapeutic Advances in Infectious Disease, 8, 20499361211042477. https://doi.org/10.1177/20499361211042477
  26. Ogba, O. M., Abia-Bassey, L. N., & Epoke, J. (2013). The relationship between opportunistic pulmonary fungal infections and CD4 count levels among HIV-seropositive patients in Calabar, Nigeria. Transactions of the Royal Society of Tropical Medicine and Hygiene, 107(3), 170-175. https://doi.org/10.1093/trstmh/trs025
  27. Pendleton, K. M., Huffnagle, G. B., & Dickson, R. P. (2017). The significance of Candida in the human respiratory tract: our evolving understanding. Pathogens and Disease, 75(3), ftx029. https://doi.org/10.1093/femspd/ftx029
  28. Prakash, H., & Chakrabarti, A. (2019). Global epidemiology of mucormycosis. Journal of Fungi, 5(1), 26. https://doi.org/10.3390/jof5010026
  29. Puebla, L. E. J. (2012). Fungal infections in immunosuppressed patients. Immunodeficiency.
  30. Rafat, Z., Hashemi, S. J., Ashrafi, K., Nikokar, I., Jafari, A., Foroushani, A. R., ... & Najar-Shahri, N. (2020). Fungal isolates of the respiratory tract in symptomatic patients hospitalized in pulmonary units: a mycological and molecular epidemiologic study. Journal of Multidisciplinary Healthcare, 13, 661. https://doi.org/10.2147%2FJMDH.S252371
  31. Rampini, S. K., Zbinden, A., Speck, R. F., & Bloemberg, G. V. (2016). Similar efficacy of broad-range ITS PCR and conventional fungal culture for diagnosing fungal infections in non-immunocompromised patients. BMC microbiology, 16(1), 1-8. https://doi.org/10.1186/s12866-016-0752-1
  32. Rodrigues, C. F., Rodrigues, M. E., & Henriques, M. (2019). Candida sp. infections in patients with diabetes mellitus. Journal of Clinical Medicine, 8(1), 76. https://doi.org/10.3390/jcm8010076
  33. Roohani, A. H., Fatima, N., Shameem, M., Khan, H. M., Khan, P. A., & Akhtar, A. (2018). Comparing the profile of respiratory fungal pathogens amongst immunocompetent and immunocompromised hosts, their susceptibility pattern and correlation of various opportunistic respiratory fungal infections and their progression in relation to the CD4+ T-cell counts. Indian journal of medical microbiology, 36(3), 408-415. https://doi.org/10.4103/ijmm.IJMM_18_258
  34. Sani, F. M., Uba, A., Tahir, F., Abdullahi, I. N., Adekola, H. A., Mustapha, J., ... & Daneji, I. M. (2020). Spectrum of pulmonary fungal pathogens, associated risk factors, and anti-fungal susceptibility pattern among persons with presumptive tuberculosis at Gombe, Nigeria. International Journal of Mycobacteriology, 9(2), 144. https://doi.org/10.4103/ijmy.ijmy_46_20
  35. Saud, B., Bajgain, P., Paudel, G., Shrestha, V., Bajracharya, D., Adhikari, S., ... & Awasthi, M. S. (2020). Fungal infection among diabetic and nondiabetic individuals in Nepal. Interdisciplinary Perspectives on Infectious Diseases, 2020. https://doi.org/10.1155/2020/7949868
  36. Shamly, V., Kali, A., Srirangaraj, S., & Umadevi, S. (2014). Comparison of microscopic morphology of fungi using lactophenol cotton blue (LPCB), iodine glycerol and congo red formaldehyde staining. Journal of clinical and diagnostic research: JCDR, 8(7), DL01. https://doi.org/10.7860%2FJCDR%2F2014%2F8521.4535
  37. Spahr, J., Weiner, D. J., Stokes, D. C., & Kurland, G. (2019). Pulmonary disease in the pediatric patient with acquired immunodeficiency states. In Kendig's Disorders of the Respiratory Tract in Children (pp. 923-943). Elsevier. https://doi.org/10.1016/B978-0-323-44887-1.00064-X
  38. Srinivas, S., Kumari, P., & Gupta, D. K. (2021). Utility of Panfungal PCR in the diagnosis of invasive fungal infections in febrile neutropenia. Journal of Family Medicine and Primary Care, 10(7), 2533. https://doi.org/10.4103%2Fjfmpc.jfmpc_2325_20
  39. Vilgalys, R., & Gonzalez, D. (1990). Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola. Current Genetics, 18(3), 277-280. https://doi.org/10.1007/BF00318394
  40. Wagner, K., Springer, B., Pires, V. P., & Keller, P. M. (2018). Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Scientific reports, 8(1), 1-7. https://doi.org/10.1038/s41598-018-25129-w
  41. Wood, R. E. (2019). Bronchoscopy and bronchoalveolar lavage in pediatric patients. Kendig's Disorders of the Respiratory Tract in Children, 134-146. https://doi.org/10.1016/B978-0-323-44887-1.00009-2
  42. Xu, L., Chen, B., Wang, F., Wei, C., Liu, H., Liu, J., ... & Luo, F. (2019). A higher rate of pulmonary fungal infection in chronic obstructive pulmonary disease patients with influenza in a large tertiary hospital. Respiration, 98(5), 391-400. https://doi.org/10.1159/000501410
  43. Yadav, S., Saxena, A., Capoor, M., & Ramesh, V. (2013). Comparison of direct microscopic methods using potassium hydroxide, periodic acid Schiff, and calcofluor white with culture in the diagnosis of onychomycosis. Indian Journal of Dermatology, Venereology, and Leprology, 79(2), 242-242.
  44. Zarrinfar, H., Mirhendi, H., Fata, A., Khodadadi, H., & Kordbacheh, P. (2015). Detection of Aspergillus flavus and A. fumigatus in bronchoalveolar lavage specimens of hematopoietic stem cell transplants and hematological malignancies patients by real-time polymerase chain reaction, nested PCR and mycological assays. Jundishapur Journal of Microbiology, 8(1). https://doi.org/10.5812%2Fjjm.13744


No citation yet. Please check again later.
How to Cite:
Rashied, H. J., Al-Attraqchi, A. A., & Muhmmed, A. K. (2022). Conventional PCR versus Culture Method to Detect Common Fungal Pathogens in Patients with Respiratory Diseases. Biomedicine and Chemical Sciences1(4), 225–233. https://doi.org/10.48112/bcs.v1i4.235
 
Publisher’s Note:
International Research and Publishing Academy (iRAPA) stands neutral with regard to jurisdictional claims in the published maps and institutional affiliations.
 
Copyright:
© 2022 Biomedicine and Chemical Sciences published by International Research and Publishing Academy (iRAPA) - Pakistan Co-published by Al-Furat Al-Awsat Technical University - Iraq
 
This is an Open Access article published under the Creative Commons Attribution 4.0 International (CC BY 4.0) (https://creativecommons.org/licenses/by/4.0/)
Creative Commons Attribution (CC BY): lets others distribute and copy the article, to create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text or data mine the article, even for commercial purposes, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, and do not modify the article in such a way as to damage the author's honour or reputation.