Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of<i>Bordetella pertussis</i>in Hospitalized Infants

Nunes, Marta C.; Soofie, Nasiha; Downs, Sarah; Tebeila, Naume; Mudau, Azwi; Gouveia, Linda de; Madhi, Shabir А.

doi:10.1093/cid/ciw521

Cited by 10 publications

(7 citation statements)

References 29 publications

(33 reference statements)

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“…In the recent work, we also observed a 4% increase in sputum yields beyond OPS. Although the diagnostic detection of sputum specimen may not be sufficient to offset mild invasive procedure, sputum samples are still important in cases with certain pathogens are suspected, such as B. pertussis [20], M. pneumoniae [4, 13, 21–23]. In this study, the advantages of sputum as a specimen type for detection of M. pneumoniae and C. pneumoniae were concordant with previous findings.…”

Section: Discussionsupporting

confidence: 89%

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

Wang

Yang

Yan

et al. 2019

Virol J

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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.

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Section: Discussionsupporting

confidence: 89%

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

Wang

Yang

Yan

et al. 2019

Virol J

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“…Neither aspirate-wash versus swab for Bordetella pertussis PCR nor non-typable Haemophilus influenzae in culture yielded a significant advantage [42,43]. Collated sensitivities of the Naclerio method vs. NPS for a variety of species in 24 healthy British adults favored NPS for Neisseria (60.2%/100%), Diptherioids (66.7%/100%), and Alphahaemolytic streptococci (18.8%/100%, p < 0.001), the Naclerio method for Staphylococcus aureus (100%/66.7%), and equivocal for Moraxella catarrhallis [33].…”

Section: Bacteriologymentioning

confidence: 94%

Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

2021

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Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.

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“…87 Two South African studies also found an increased yield of B pertussis on PCR with induced sputum, 11 88 although no difference was shown in another hospital based study. 89 Several studies have shown good agreement between PCR testing of induced sputum and nasopharyngeal swabs for viruses; the yield is highest when both sample types are tested. The use of induced sputum has also been reported to be helpful for microbiologic confirmation of Pneumocystis jirovecii pneumonia in HIV infected children when using PCR for diagnosis.…”

Section: Respiratory Samplesmentioning

confidence: 99%

Advances in the diagnosis of pneumonia in children

Zar

Andronikou

Nicol

2017

BMJ

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Pneumonia remains a major cause of childhood mortality and morbidity globally. Accurate diagnosis and attribution of the causes of pneumonia are important for measuring the burden of disease, implementing appropriate preventive or treatment strategies, and developing more effective interventions. This review summarizes recent diagnostic advances in radiological techniques, specimen collection, and laboratory methods. Although chest ultrasound and chest magnetic resonance imaging are promising modalities for radiological diagnosis, their role in clinical management and their impact on outcomes need further study. Rapid, highly sensitive, multiplex laboratory tests performed on upper respiratory tract samples or induced sputum can detect nucleic acid from potential pathogens in most children with pneumonia. However, it may be difficult to attribute causality because it is often impossible to distinguish between organisms colonizing or infecting the upper respiratory tract and those causing pneumonia. Currently available host biomarkers lack accuracy for distinguishing bacterial or mixed bacterial-viral infections from viral infections. New biomarkers derived from host transcriptional profile analysis may be more accurate but require validation. Prospective studies with appropriate control populations, including studies of clinical impact, are needed to improve our understanding of the role of tests. Although progress has been made in radiological techniques and laboratory testing, current methods for diagnosing and attributing the causes of pneumonia are suboptimal.

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Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection ofBordetella pertussisin Hospitalized Infants

Cited by 10 publications

References 29 publications

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

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

Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

Advances in the diagnosis of pneumonia in children

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