Spectrum of Respiratory Pathogens Diagnosed by Multiplex-PCR in Suspected Cases of Atypical Pneumonia in a Tertiary Care Hospital of Bangladesh

Background

Pneumonia is one of the most common causes of death worldwide. The urgent and clinical heterogeneity of this infection results in dilemma of diagnosis and treatment. There is inconsistency in the definition of the group of microorganisms that cause “atypical pneumonia.” Nevertheless, the use of this term in the medical and radiologic literature is common. Among the causes of community acquired pneumonia, atypical bacteria are responsible for approximately 15% of cases. Zoonotic and nonzoonotic bacteria, as well as viruses, have been considered among the causes of atypical pneumonia in a patient who is immunocompetent and have been associated with major community outbreaks of respiratory infection, with relevant implications in public health policies.

Methods

A total of 114 samples from Combined Military Hospital, Dhaka Cantonment was tested at Armed Forces Institute of Pathology, Dhaka Cantonment during the period of January to December 2022. Sputum, bronchial wash, nasal and throat swab was collected and tested by QIAstat-Dx Multiplex-PCR system.

Results

Among 114 samples 27 (23.65%) was found positive for various respiratory pathogen. Total 34 pathogen was detected as 22 samples found positive with single organism and 5 samples found positive with multiple organism. Rhinovirus was detected as the most prevalent organism (20.58%) followed by Influenza A H3 (14.70%), Parainfluenza, Enterovirus and Adenovirus (11.76%), Coronavirus 229E, SARS-CoV-2 and Human Metapneumovirus A/B (5.88%), Coronavirus OC43, Respiratory Syncytial Virus A/B and Bocavirus (2.94%). Mycoplasma pneumoniae (2.94%) was found only bacteria among collected samples.

Conclusion

Multiplex real-time RT-PCR system is an excellent tool for rapid diagnosis of large number of respiratory pathogen and provides detail genetic information to clinician to start the management immediately. The assay exhibited improvements to sensitivity, specificity, time and cost-effectiveness compared to previous assays utilised for clinical and epidemiological applications.