LSplex #

LSplex would amplify selectively the underrepresented bacterial DNA. The large set of primer pairs is potentially able to amplify as many gene segments as probes are Quisinostat mw immobilized on the prototype microarray but in practice, it is supposed to only amplify the gene-segments specific to the pathogens present in the analyte.

In parallel, real-time PCR-based assays for identification of pathogens were proposed since the sensitivity is adequate for direct detection and quantification [10–12, 40–43]. However, the information level obtained by this approach is incomparably lower than the one provided by medium or high density microarray analyses. Real-time PCR has a reduced potential for multiplexing because the current availability of only four to five channels for the simultaneous non-overlapping detection of different fluorophores [21]. For this reason, real-time PCR is in general confined to a mere species identification based on single sequence polymorphism [10, 43] or to confirm the presence of a suspected pathogen by using a reduced number of specific primer pairs [44, 45] eventually completed by the detection of a few genes related to antibiotic resistance [46, 45]. In contrast, microarrays offer the possibility to profile pathogens by providing information at the strain level [36],

by detecting virulence factors and genes determining the antibiotic resistance [16]. The LSplex amplification protocol is a promising co-adjuvant for pathogen KU55933 supplier profiling by microarray analysis since it increases sensitivity and the specificity

of detection. It also presents the flexibility of using hundreds of primer pairs, whose sequences Ribose-5-phosphate isomerase are exchangeable in function of the pathogens targeted in the microarray. The single-step LSplex protocol, allowing labelling during amplification, could represent one piece of the methodological mosaic in a future time-saving bacteriological diagnostic approach. Acknowledgements We are grateful to Georg Plum and Paul Higgins for helpful comments on the manuscript. This work was supported by the DFG, the DFG Gottfried-Wilhelm-Leibniz-Program, the GEW Stiftung, Cologne, Germany and Köln Fortune. Electronic supplementary material Additional file 1: Microarray probes and primer sequences. The table contains the description of microarray probes and primer sequences used in the study. (PDF 73 KB) Additional file 2: Prototype DNA microarray for detection of common pathogens. The figure represents the analysis of microarray hybridizations with decreasing amounts of bacterial DNA. (PDF 602 KB) References 1. Cho JC, Tiedje JM: Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol 2002, 68:1425–1430.CrossRefPubMed 2. Cleven BE, Palka-Santini M, Gielen J, Meembor S, Krönke M, Krut O: Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J Clin Microbiol 2006, 44:2389–2397.CrossRefPubMed 3.

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