Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay

• Published in: Journal of Clinical Microbiology 2007-02, Vol.45 (2), p.443-452
• Main Authors: Lin, Baochuan, Blaney, Kate M, Malanoski, Anthony P, Ligler, Adam G, Schnur, Joel M, Metzgar, David, Russell, Kevin L, Stenger, David A
• Format: Article
• Language: English
• Subjects: Algorithms; Avian influenza virus; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacterial Infections - microbiology; Bacterial Typing Techniques; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Humans; Infectious diseases; Medical sciences; Microbiology; Oligonucleotide Array Sequence Analysis; Pharynx - microbiology; Pharynx - virology; Polymerase Chain Reaction; Predictive Value of Tests; Respiratory Tract Infections - microbiology; Respiratory Tract Infections - virology; Sensitivity and Specificity; Sequence Analysis, DNA - methods; Virology; Virus Diseases - virology; Viruses - classification; Viruses - genetics; Viruses - isolation & purification
• ISSN: 0095-1137; 1098-660X; 1098-5530
• DOI: 10.1128/jcm.01870-06

Simultaneous testing for detection of infectious pathogens that cause similar symptoms (e.g., acute respiratory infections) is invaluable for patient treatment, outbreak prevention, and efficient use of antibiotic and antiviral agents. In addition, such testing may provide information regarding possible coinfections or induced secondary infections, such as virally induced bacterial infections. Furthermore, in many cases, detection of a pathogen requires more than genus/species-level resolution, since harmful agents (e.g., avian influenza virus) are grouped with other, relatively benign common agents, and for every pathogen, finer resolution is useful to allow tracking of the location and nature of mutations leading to strain variations. In this study, a previously developed resequencing microarray that has been demonstrated to have these capabilities was further developed to provide individual detection sensitivity ranging from 10¹ to 10³ genomic copies for more than 26 respiratory pathogens while still retaining the ability to detect and differentiate between close genetic neighbors. In addition, the study demonstrated that this system allows unambiguous and reproducible sequence-based strain identification of the mixed pathogens. Successful proof-of-concept experiments using clinical specimens show that this approach is potentially very useful for both diagnostics and epidemic surveillance.