Target amplification for broad spectrum microbial diagnostics and detection

被引:9
作者
Leski, Tomasz A. [1 ,2 ]
Malanoski, Anthony P. [1 ]
Stenger, David A. [1 ]
Lin, Baochuan [1 ]
机构
[1] USN, Res Lab, Ctr Bio Mol Sci & Engn, Washington, DC 20375 USA
[2] Nova Res Inc, Alexandria, VA USA
关键词
16S rRNA; microarrays; multiplex PCR; random amplification; small subunit rRNA; strand displacement amplification; whole genome amplification; WHOLE-GENOME AMPLIFICATION; 16S RIBOSOMAL-RNA; MICROARRAY-BASED DETECTION; MULTIPLE DISPLACEMENT AMPLIFICATION; RESPIRATORY-TRACT INFECTIONS; BASE STACKING HYBRIDIZATION; OLIGONUCLEOTIDE MICROARRAY; DNA MICROARRAY; PATHOGEN DETECTION; BACTERIAL PATHOGENS;
D O I
10.2217/FMB.09.126
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification, This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques, The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
引用
收藏
页码:191 / 203
页数:13
相关论文
共 124 条
[1]   Environmental whole-genome amplification to access microbial populations in contaminated sediments [J].
Abulencia, Carl B. ;
Wyborski, Denise L. ;
Garcia, Joseph A. ;
Podar, Mircea ;
Chen, Wenqiong ;
Chang, Sherman H. ;
Chang, Hwai W. ;
Watson, David ;
Brodie, Eoln L. ;
Hazen, Terry C. ;
Keller, Martin .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2006, 72 (05) :3291-3301
[2]   Hybridization of genomic DNA to microarrays:: A challenge for the analysis of environmental samples [J].
Avarre, Jean-Christophe ;
de Lajudie, Philippe ;
Bena, Gilles .
JOURNAL OF MICROBIOLOGICAL METHODS, 2007, 69 (02) :242-248
[3]   Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria [J].
Bae, JW ;
Rhee, SK ;
Park, JR ;
Chung, WH ;
Nam, YD ;
Lee, I ;
Kim, H ;
Park, YH .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2005, 71 (12) :8825-8835
[4]   Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel [J].
Barker, DL ;
Hansen, MST ;
Faruqi, AF ;
Giannola, D ;
Irsula, OR ;
Lasken, RS ;
Latterich, M ;
Makarov, V ;
Oliphant, A ;
Pinter, JH ;
Shen, R ;
Sleptsova, I ;
Ziehler, W ;
Lai, E .
GENOME RESEARCH, 2004, 14 (05) :901-907
[5]   Portable system for microbial sample preparation and oligonucleotide microarray analysis [J].
Bavykin, SG ;
Akowski, JP ;
Zakhariev, VM ;
Barsky, VE ;
Perov, AN ;
Mirzabekov, AD .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2001, 67 (02) :922-928
[6]   Massively parallel pathogen identification using high-density microarrays [J].
Berthet, Nicolas ;
Dickinson, Philip ;
Filliol, Ingrid ;
Reinhardt, Anita K. ;
Batejat, Christophe ;
Vallaeys, Tatiana ;
Kong, Katherine A. ;
Davies, Christopher ;
Lee, Walter ;
Zhang, Shenglan ;
Turpaz, Yaron ;
Heym, Beate ;
Coralie, Gilberte ;
Dacheux, Laurent ;
Burguiere, Ana Maria ;
Bourhy, Herve ;
Old, Iain G. ;
Manuguerra, Jean-Claude ;
Cole, Stewart T. ;
Kennedy, Giulia C. .
MICROBIAL BIOTECHNOLOGY, 2008, 1 (01) :79-86
[7]   Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR [J].
Berthet, Nicolas ;
Reinhardt, Anita K. ;
Leclercq, India ;
van Ooyen, Sven ;
Batejat, Christophe ;
Dickinson, Philip ;
Stamboliyska, Rayna ;
Old, Iain G. ;
Kong, Katherine A. ;
Dacheux, Laurent ;
Bourhy, Herve ;
Kennedy, Giulia C. ;
Korfhage, Christian ;
Cole, Stewart T. ;
Manuguerra, Jean-Claude .
BMC MOLECULAR BIOLOGY, 2008, 9
[8]   Oligonucleotide microarrays in microbial diagnostics [J].
Bodrossy, L ;
Sessitsch, A .
CURRENT OPINION IN MICROBIOLOGY, 2004, 7 (03) :245-254
[9]   A METHOD FOR THE RAPID SEQUENCE-INDEPENDENT AMPLIFICATION OF MICRODISSECTED CHROMOSOMAL MATERIAL [J].
BOHLANDER, SK ;
ESPINOSA, R ;
LEBEAU, MM ;
ROWLEY, JD ;
DIAZ, MO .
GENOMICS, 1992, 13 (04) :1322-1324
[10]   DNA microarrays for virus detection in cases of central nervous system infection [J].
Boriskin, YS ;
Rice, PS ;
Stabler, RA ;
Hinds, J ;
Al-Ghusein, H ;
Vass, K ;
Butcher, PD .
JOURNAL OF CLINICAL MICROBIOLOGY, 2004, 42 (12) :5811-5818