title: Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays.
abstract: We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant sequences. This improvement was attributed to the lower sequence divergence of RASs, which also expanded the sequence space covered by the microarray. Extension of this novel microarray design strategy to viruses, antimicrobial resistance elements or toxins is straightforward.
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Berthet
authors.forename: Alexis
authors.initials: A
authors.lastname: Deletoile
authors.forename: Virginie
authors.initials: V
authors.lastname: Passet
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Manuguerra
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000737:chemistry; D015373:Bacterial Typing Techniques; D012321:DNA-Directed RNA Polymerases; D030562:Databases, Protein; D024881:Drug Resistance, Bacterial; D004755:Enterobacteriaceae / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C540081:rpoB protein, E coli; D012321:DNA-Directed RNA Polymerases