Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays

Nicolas Berthet (1, 2) , Alexis Deletoile (1) , Virginie Passet (1) , Giulia C. Kennedy (3) , Jean-Claude Manuguerra (4) , Stewart T. Cole (5) , Sylvain Brisse (1)

1 PF8 - Génotypage des Pathogènes et Santé Publique (Plate-forme)
2 Epidémiologie et Physiopathologie des Virus Oncogènes
3 Affymetrix
4 CIBU - Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats
5 EPFL - Ecole Polytechnique Fédérale de Lausanne

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.

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Microbiology and Parasitology; Life Sciences [q-bio]; Microbiology and Parasitology; Virology

Nicolas Berthet, Alexis Deletoile, Virginie Passet, Giulia C. Kennedy, Jean-Claude Manuguerra, et al.. Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays. PLoS ONE, 2010, 5 (12), pp.e15243. ⟨10.1371/journal.pone.0015243⟩. ⟨pasteur-03516001⟩