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

Abstract

a b s t r a c tObjectives: 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%e69%) and 50% (95% CI 39%e61%) for comprehensive molecular testing, and 14% (95% CI 82%e21%) and 94% (95% CI 86%e98%) 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).

Community-acquired bacterial pneumonia in adults

“…This system has been tested on BAL samples in ICU patients and shown to increase pathogen detection and positive predictive value in diagnosing Gram-negative bacteria with a sensitivity and specificity of 68.4 and 86 per cent 86 . Another multiplex PCR, Fast Track Diagnostics FTD-29.19, tests nine bacterial pathogens and has demonstrated more pathogen detection in 37 per cent over 11 per cent by conventional methods in elderly patients 87 . Multiplexing several gene targets for detection of atypical pathogens has shown comparable performance with in-house individual PCRs in a study demonstrating overall 52 per cent PCR positivity in patients suspected with atypical pneumonia 88 .…”

Undetected Causes of Death in Hospitalized Elderly with COVID-19: Lessons from Autopsy

“…However, the diagnostic of pneumonia in elderly patients is challenging because symptoms are less specific and decompensated comorbidities are frequently associated [ 27 ]. The differentiation between viral versus bacterial pneumonia may also be difficult as the microorganism causing bacterial pneumonia is identified in only a minority of patients [ 28 ]. Patient 2 did not receive antibiotic but signs of bacterial pneumonia were finally found on the autopsy.…”

Severe influenza/respiratory syncytial virus infections and hospital antimicrobial stewardship opportunities: impact of a 4-year surveillance including molecular diagnosis

“…15 Recent studies assessing the impact of a viral diagnosis on antimicrobial management in hospitalized adults remain inconclusive or present a wide range of designs with mixed results. [16][17][18][19][20][21][22][23][24][25] Furthermore, influenza and RSV illness severity patterns are not necessarily associated with bacterial coinfections (eg, in older patients and/or patients with comorbidities). A positive viral diagnosis can therefore help clinicians to decide whether to withhold or discontinue antibiotic treatment based on patient medical history, clinical presentation, and available bacterial investigations results.…”