Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection

Abstract

Background Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS). Methods Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum. Results From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum ( p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24) . Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results ( p = .002). Conclusions Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae . Young patients are likely to have consistent results between the two specimens. Electronic supplementary material The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.

Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay

“…Currently, nucleic acid amplification techniques (NAATs) (such as PCR and multiplex PCR) have been increasingly used for identification of pathogens in infectious respiratory diseases; and one of the multiplex‐PCR technology, GenomeLab gene expression profiler genetic analysis system (GeXP)‐based assay (developed by Beckman Coulter), has been adopted in the infectious pathogens diagnostics; this detection technique has been applied in clinical for over 5 years; however, more clinical application studies are still necessary, especially in southeast China. GenomeLab gene expression profiler genetic analysis system is a high‐sensitive and specific analytical platform for high‐throughput nucleic acid detection based on capillary electrophoresis separation technology, multiple gene analysis technology, and high‐sensitivity laser‐induced fluorescence technology .…”

Immunochromatography for the diagnosis of Mycoplasma pneumoniae infection: A systematic review and meta-analysis

“…The authors suspected the reasons for their findings was due to varied M. pneumoniae density in the NP swab specimens, which were collected in a blinded fashion, and the larger OP swab tip, which was able to reach deeper into the airway resulting in a specimen higher load of M. pneumoniae. In addition, it has been reported that a higher copy number of M. pneumoniae is found in the alveoli than on the epithelium of the upper respiratory tract [78,79].…”

Evaluation of two commercial multiplex PCR tests for the diagnosis of acute respiratory infections in hospitalized children

“…An increasing number of recently published studies focus on the development of molecular methods to solve multiple detection in one reaction [5,13,14,18,19]. The multiplex-PCR methods has been previously evaluated versus conventional techniques [1,6,8,20] or single-plex PCR [21].…”

“…DNA/RNA extraction is performed on an automated workstation (Smart LabAssist-16/32, Health Gene Technologies, China) [14]. A total of 200µL of lique ed sputum was used for nucleic acid extraction and eluted in 30µL, which was divided into two parts for ResP-CE and XYres-MCA analysis, respectively.…”

“…A total of 200µL of lique ed sputum was used for nucleic acid extraction and eluted in 30µL, which was divided into two parts for ResP-CE and XYres-MCA analysis, respectively. ResP-CE analysis has been described in previous work, and we performed the experiments according to previously reported methods [14].…”