Hybridization capture and next generation sequencing of Treponema pallidum in non-human primate bone samples

We generated DNA extracts from non-lesioned NHP bones (N=51, 6 species from Taï National Park, Côte d'Ivoire) and first screened them with three independent PCR systems specific to T. pallidum. No bone was positive for all three PCR systems, suggesting T. pallidum DNA is highly fragmented or at low concentrations. Based on this screening, we selected three candidate extracts for which we conducted library preparation, enrichment, and sequencing in separate laboratories. At the University of Tübingen we used a DNA microarray-based approach and post-capture pathogen enriched DNA was sequenced on an Illumina HiSeq 2500. At the Robert Koch Institute, we used an in-solution capture approach and post-capture pathogen enriched DNA was sequenced on an Illumina MiSeq.