Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods.

Autor:	Bartlow AW; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Stromberg ZR; Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Gleasner CD; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Hu B; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Davenport KW; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Jakhar S; Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Li PE; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Vosburg M; Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America., Garimella M; Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America., Chain PSG; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Erkkila TH; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Fair JM; Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Mukundan H; Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
Jazyk:	angličtina
Zdroj:	PLOS global public health [PLOS Glob Public Health] 2022 Jul 20; Vol. 2 (7), pp. e0000811. Date of Electronic Publication: 2022 Jul 20 (Print Publication: 2022).
DOI:	10.1371/journal.pgph.0000811
Abstrakt:	Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks. Competing Interests: The authors have declared that no competing interests exist. (Copyright: © 2022 Bartlow et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze:	MEDLINE
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