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Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay

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Abstract

The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.

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Acknowledgments

We would be appreciative of Baqiyatallah University of Medical Sciences and Ghaem hospital laboratory stuff for their generous cooperation.

Funding

This work was financially supported by a Grant (no. 971776) from Research Council of Mashhad University of Medical Sciences, Mashhad, Iran.

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Authors and Affiliations

  1. Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran

    Reza Kamali Kakhki & Kiarash Ghazvini

  2. Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Mohammad Javad Najafzadeh

  3. Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran

    Reza Kachuei

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  1. Reza Kamali Kakhki
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  2. Mohammad Javad Najafzadeh
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  3. Reza Kachuei
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  4. Kiarash Ghazvini
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Correspondence to Reza Kachuei.

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The authors have declared that they have no conflict of interest.

Ethics approval and consent to participate

The ethical approval for performing this study was obtained from the Ethics Committee of the Mashhad University of Medical Sciences (Ethics code of IR.MUMS.MEDICAL.REC.1398.529), and written informed consent was obtained from participants.

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Co-first author: Reza Kamali Kakhki, Mohammad Javad Najafzadeh

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Kamali Kakhki, R., Najafzadeh, M.J., Kachuei, R. et al. Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay. Eur J Clin Microbiol Infect Dis 39, 1535–1542 (2020). https://doi.org/10.1007/s10096-020-03879-8

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  • DOI: https://doi.org/10.1007/s10096-020-03879-8

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