Rapid identification viruses from nasal pharyngeal aspirates in acute viral respiratory infections by RT-PCR and electrospray ionization mass spectrometry

Abstract

Diagnosis of the etiologic agent of respiratory viral infection relies traditionally on culture or antigen detection. This pilot was conducted evaluation comparing performance characteristics of the RT-PCR and Electrospray Ionization Mass Spectrometry (RT-PCR/ESI-MS) platform to conventional virological methods for identifying multiple clinically relevant respiratory viruses in nasopharyngeal aspirates. The RT-PCR/ESI-MS respiratory virus surveillance kit was designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1-4, adenoviridae types A-F, coronaviridae, human bocavirus, and human metapneumovirus. Patients (N=192) attending an emergency department during the 2007-8 respiratory season consented, and “excess” frozen archived nasopharyngeal aspirates were analysed; 46 were positive by conventional virology and 69 by RT-PCR/ESI-MS, among which there were six samples with multiple viral pathogens detected. The sensitivity and specificity of the assay were 89.1% and 80.3%, respectively. Additional viruses that were not identified by conventional virology assays were detected (4 human bocaviruses and 7 coronaviruses). Samples in which the RT-PCR/ESI-MS results disagreed with conventional virology were sent for analysis by a third method using a commercial RT-PCR-based assay, which can identify viruses not detectable by conventional virologic procedures. Time to first result of RT-PCR/ESI-MS was 8 hours. RT-PCR/ESI-MS demonstrated capacity to detect respiratory viruses identifiable and unidentifiable by conventional methods rapidly.

Detection, Identification, and Distribution of Fungi in Bronchoalveolar Lavage Specimens by Use of Multilocus PCR Coupled with Electrospray Ionization/Mass Spectrometry

“…This method enables detection and identification of causative pathogens directly from clinical specimens or mixtures of organisms with rapid turnaround and high throughput (9,10). This technique has been used to detect bacteria, viruses, yeasts, and other infectious agents (10)(11)(12)(13), but there are no data on its value for the detection of fungal organisms, including yeasts and molds.…”

Mass spectrometry: a revolution in clinical microbiology?

“…Although this technology needs to be validated more extensively, there are some recent publications on the detection of Aspergillus terreus from bronchio-alveolar lavage [61] and a panel of respiratory viruses from nasopharyngeal aspiration that represents an important target for the future in clinical microbiology [62] .…”

Rethinking Approaches to Improve the Utilization of Nucleic Acid Amplification Tests for Detection and Characterization of Influenza A in Diagnostic and Reference Laboratories

“…These tools allow for the characterization of pathogen diversity within the host, allow for assay flexibility that is not susceptible to constant mutations, and may be worked into a high throughput workflow. Approaches such as RT-PCR/electrospray ionization mass spectrometry for characterization of IFVA are promising [165][166][167][168].…”