Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

V Prendki; B Huttner; C Marti; A Mamin; P E Fubini; M P Meynet; M Scheffler; X Montet; J P Janssens; J L Reny; L Kaiser; N Garin; J Stirnemann

doi:10.1016/j.cmi.2018.12.037

Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

Clin Microbiol Infect. 2019 Sep;25(9):1114-1119. doi: 10.1016/j.cmi.2018.12.037. Epub 2019 Jan 12.

Authors

V Prendki¹, B Huttner², C Marti³, A Mamin⁴, P E Fubini⁵, M P Meynet⁶, M Scheffler⁷, X Montet⁸, J P Janssens⁹, J L Reny¹⁰, L Kaiser², N Garin¹¹, J Stirnemann¹²

Affiliations

¹ ()) Division of Internal Medicine and Rehabilitation, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland; ()) Faculty of Medicine, University of Geneva, Switzerland. Electronic address: virginie.prendki@hcuge.ch.
² ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Division of Infectious Diseases, Geneva University Hospitals, Switzerland.
³ ()) Division of General Internal Medicine, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland.
⁴ ()) Division of Infectious Diseases, Geneva University Hospitals, Switzerland.
⁵ ()) Division of Internal Medicine and Rehabilitation, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland; ()) Division of General Internal Medicine, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland.
⁶ ()) Division of Internal Medicine and Rehabilitation, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland.
⁷ ()) Department of Radiology, Geneva University Hospitals, Switzerland.
⁸ ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Department of Radiology, Geneva University Hospitals, Switzerland.
⁹ ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Department of Pneumology, Geneva University Hospitals, Switzerland.
¹⁰ ()) Division of Internal Medicine and Rehabilitation, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland; ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Division of General Internal Medicine, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland.
¹¹ ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Division of General Internal Medicine, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland; ()) Department of General Internal Medicine, Riviera Chablais Hospitals,Monthey, Switzerland.
¹² ()) Faculty of Medicine, University of Geneva, Switzerland; ()) Division of General Internal Medicine, Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, Switzerland.

Abstract

Objectives: We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals.

Methods: We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists.

Results: The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%-69%) and 50% (95% CI 39%-61%) for comprehensive molecular testing, and 14% (95% CI 82%-21%) and 94% (95% CI 86%-98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing.

Conclusion: Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192).

Clinical trials registration: NCT02467192.

Keywords: Diagnosis; Elderly patients; Low-dose CT scan; Multiplex PCR; Nasopharyngeal swabs; Pneumonia.

Publication types

Clinical Trial
Comparative Study

MeSH terms

Aged
Aged, 80 and over
Cohort Studies
Diagnostic Tests, Routine
Humans
Microbiological Techniques / standards*
Pharynx / microbiology*
Pharynx / virology*
Pneumonia / diagnosis*
Pneumonia / microbiology
Pneumonia / virology
Polymerase Chain Reaction / standards*
Prospective Studies
Sensitivity and Specificity
Tomography, X-Ray Computed

Associated data

ClinicalTrials.gov/NCT02467192