Abstract:
:The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.
journal_name
Genome Resjournal_title
Genome researchauthors
Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DAdoi
10.1101/gr.4337206subject
Has Abstractpub_date
2006-04-01 00:00:00pages
527-35issue
4eissn
1088-9051issn
1549-5469pii
gr.4337206journal_volume
16pub_type
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