Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.
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.
Lin
Baochuan
B
Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, District of Columbia 20375, USA.
Wang
Zheng
Z
Vora
Gary J
GJ
Thornton
Jennifer A
JA
Schnur
Joel M
JM
Thach
Dzung C
DC
Blaney
Kate M
KM
Ligler
Adam G
AG
Malanoski
Anthony P
AP
Santiago
Jose
J
Walter
Elizabeth A
EA
Agan
Brian K
BK
Metzgar
David
D
Seto
Donald
D
Daum
Luke T
LT
Kruzelock
Russell
R
Rowley
Robb K
RK
Hanson
Eric H
EH
Tibbetts
Clark
C
Stenger
David A
DA
D015373:Bacterial Typing Techniques / Q000379:methods; D006801:Humans; D016533:Mycological Typing Techniques / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016133:Polymerase Chain Reaction; D011237:Predictive Value of Tests; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods