Diagnostic performance of an in-house multiplex PCR assay and the retrospective surveillance of bacterial respiratory pathogens at a teaching hospital, Kelantan, Malaysia

ABSTRACT

Respiratory tract infections (RTIs), including pneumonia and pulmonary tuberculosis, are among the leading causes of death worldwide. The use of accurate diagnostic tests is crucial to initiate proper treatment and therapy to reduce the mortality rates for RTIs. A PCR assay for simultaneous detection of six respiratory bacteria: Haemophilus influenzae, Klebsiella pneumoniae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae, was developed in our lab. The current study aimed to evaluate the performance of this assay along with the retrospective surveillance of respiratory pathogens at a teaching hospital in Kelantan, Malaysia. Leftover sputa (n = 200) from clinical laboratories were collected and undergone DNA template preparation for PCR analysis. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the PCR assay were determined in comparison with the gold standard sputum culture. Overall, the accuracy performance of this assay was 94.67% (95% CI: 90.87% to 97.21%) with sensitivity, specificity, PPV and NPV of 100%, 91.67%, 87.1% and 100%, respectively. Based on the organisms detected from sputa, K. pneumoniae ranked as the top isolate (n = 48), followed by P. aeruginosa (n = 13) and H. influenzae (n = 10). Surveillance among the patients showed that the associations of bacterial positive with gender and means of acquisition were found significant (p values = 0.049 and 0.001, respectively). Besides the promising performance of this ready-to-use molecular-based assay for the rapid detection of selected bacteria pathogens, this study also highlighted significant spread of K. pneumoniae RTIs in the community.

KEYWORDS:

• Multiplex PCR
• respiratory tract infections
• community-acquired pneumonia
• Klebsiella pneumoniae
• Haemophilus influenzae
• Pseudomonas aeruginosa

Acknowledgments

The authors wish to thank the Hospital Universiti Sains Malaysia and Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, for providing the specimens, strains and facilities used in this study.

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Author contributions

Conceptualization, S.S., S.M., and H.H.; methodology, N.M.N.N.Z.; validation, N.M.N.N.Z., S.M., and S.S.; formal analysis, N.M.N.N.Z. and S.S.; writing—original draft preparation, N.M.N.N.Z.; writing—review and editing, N.M.N.N.Z., S.M., H.H., M.D.G., and S.S.; supervision, H.H., S.M., and S.S. All authors have read and agreed to the published version of the manuscript.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

The research was supported by the Ministry of Higher Education Malaysia, Long-term Research Grant Scheme (LRGS): 203.PTS.6728003, and by Universiti Sains Malaysia, Research University (RU) Grant: 1001.PPSP.8012298.