Straining Pathogen Sequences

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Science  25 May 2007:
Vol. 316, Issue 5828, pp. 1099
DOI: 10.1126/science.316.5828.1099b

Several methods have been explored as platforms for the rapid detection of infectious pathogens, including mass spectrometric analysis of amplified nucleic acid sequences and several microarray schemes. Most of these assays have been tested against a small subset of pathogens, and often do not resolve pathogen subtypes or have the ability to identify emerging strains.

Lin et al. tested a microarray, the respiratory pathogen microarray version 1 (RPM v.1), against 424 nasal wash samples collected from military personnel in the Washington, DC, area from December 2004 to February 2005 (influenza season). Human DNA and RNA were removed from these samples before carrying out a single amplification step for viral and bacterial pathogen sequences and subsequent hybridization against 20 pathogens (some of which are represented by more than one strain). Software-based reassembly of incomplete or disconnected sequences improved the identification of pathogens, with an accuracy >98% compared to independent reference assays. In the 58 specimens that contained multiple pathogens, an increase was seen in bacterial colonizers when viral infection was present. In 250 of the samples positive for influenza A, nucleotide variations in the hemagglutinin gene were identified that allowed a phylogenetic tree of strain evolution to be assembled. In 14% of the samples, pathogens were not identified, even though the patients had flu-like symptoms; this finding likely reflects the under-representation of rhinovirus and enterovirus sequences in the microarray tiles. — PDS

PLoS ONE 2, e419 (2007).

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