Abstract
BackgroundAdvances 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).MethodsEleven 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.ResultsFrom 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).ConclusionsFlocked 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.
Highlights
Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases
To compare the detection rates between sputum and oropharyngeal swabs (OPS) samples, a total of 659 hospitalized children< 13 years were enrolled from January to June of 2018
182 were excluded because: i) 8 samples were not collected by the nurses who have received a sampling training; ii) 105 patients refused to provide the pairing OPS specimens; iii) 69 sputum and OPS were not collected on the same day
Summary
Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Molecular techniques directly applied to respiratory tract specimens could detect multiple pathogens with high specificity and sensitivity [3], the choice of sample type and sampling method is critical for optimal diagnostic efficacy [4]. Lots of studies have compared the yields of these upper respiratory tract specimens, and by PCR to identify viral or bacterial infections by PCR, they have found that the sensitivity of aspirate (or suction) is greater than that of swabs [6,7,8]. Young children and parents may find this relatively invasive and distressing procedure unacceptable, limiting its use in routine clinical practice [9, 12] Those oropharyngeal suction or sputa, presumably from, or contaminated by secretions from the upper respiratory tract [13, 14]. It is important to assess the prevalence of pathogens in different types of specimens
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