Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Conclusions: Much of respiratory medicine is reliant on timely and precise diagnostics for critical treatment. However, respiratory infections remain a leading cause of global mortality and morbidity despite advances in diagnosis and treatment. In this study, we (a) compared nasopharyngeal samples from patients suspected of acute upper respiratory infection between a commercially available PCR assay and a targeted hybridization-capture-based mNGS workflow and (b) demonstrated that the hybridized approach may provide tremendous advantage in deciphering the etiological agent of respiratory (co)infections and provide clinical relevance for trafficking potential. This is important because the trafficking potential from the upper to the lower respiratory tract and infection severity depend on pathogen virulence, concomitant infections, and underlying respiratory comorbidities [81]. This is significant to respiratory medicine because this technology can be used to supplement current syndromic-based tests, and data can quickly and effectively be phenotypically characterized for clinical (co)infection and comorbid consideration. This has significance for laboratory medicine because it demonstrated that this approach can rapidly be interpreted with a user-friendly and reliable platform for collective intention without overburdening laboratory investments in technology and people [82,83]. Furthermore, this approach could be advanced into pan-microbial diagnostic testing that utilizes a single workflow for all specimen types. Although we have demonstrated the analytical advantage of a targeted hybridization-capture-based mNGS workflow over targeted PCR analysis, further investigations are required to establish the clinical relevance of phenotypic classifications and their value to trafficking predispositions and utility in respiratory medicine.