Evaluation of a multiplex PCR kit for detection of 17 respiratory pathogens in hospitalized patients

Cuiping Zhang; Xiaoyan Chen; Lu Wang; Juan Song; Chunmei Zhou; Xiaohuan Wang; Yan Ma; Cuicui Chen; Wei Guo; Yuanlin Song

doi:10.21037/jtd-22-544

Evaluation of a multiplex PCR kit for detection of 17 respiratory pathogens in hospitalized patients

J Thorac Dis. 2022 Sep;14(9):3386-3397. doi: 10.21037/jtd-22-544.

Authors

Cuiping Zhang^#¹, Xiaoyan Chen^#¹, Lu Wang¹, Juan Song¹, Chunmei Zhou², Xiaohuan Wang², Yan Ma², Cuicui Chen¹, Wei Guo², Yuanlin Song^{1

3

4

5

6}

Affiliations

¹ Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
² Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
³ Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China.
⁴ Shanghai Respiratory Research Institute, Shanghai, China.
⁵ National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
⁶ Jinshan Hospital of Fudan University, Shanghai, China.

^# Contributed equally.

Abstract

Background: Rapid pathogen identification is critical for optimizing diagnosis and treatment of infectious diseases. Multiplex polymerase chain reaction (PCR) is a sensitive, broad-spectrum molecular detection technique that is simple and rapid to perform. It is capable of simultaneously screening for multiple pathogens within a short time range. Here, we designed and evaluated a multiplex PCR kit for the identification of 17 common respiratory pathogens in clinical samples from hospitalized patients.

Methods: A total of 452 samples from hospitalized patients, including 242 respiratory and 210 non-respiratory samples, were analyzed for 13 bacteria and 4 fungi by a multiplex fluorescent PCR kit. The diagnostic performance of the kit was assessed by considering routine microbiology as the reference standard.

Results: The overall positivity rate of the multiplex PCR kit was 86.9%, much higher than that noted on routine microbiology (56.9%). Furthermore, the co-infection detection rate was also significantly higher than that noted on routine microbiology (69.5% vs. 15.0%). Compared with routine microbiology, kit sensitivity was >90% for detection of most target bacteria, with a negative predictive value (NPV) of >99%, especially for detection of Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, Stenotrophomonas maltophilia, Enterococcus faecium, Enterococcus faecalis and Escherichia coli. The kit was noted to be particularly superior in identifying Stenotrophomonas maltophilia and Streptococcus pneumoniae as compared to routine microbiology. The multiplex PCR kit was noted to be less sensitive (33.3-59.6%) and more specific (93.9-100.0%) for detection of mycobacteria and fungi.

Conclusions: Our multiplex PCR kit offers a rapid and sensitive diagnosis of common bacterial pneumonia, although sensitivity for mycobacteria and fungi warrants enhancement. Further optimization includes minimizing false positivity and increasing relevance to clinical application.

Keywords: Multiplex polymerase chain reaction (PCR); molecular diagnostics; pathogen detection; pneumonia; rapid diagnostics.