Assembly of Dense Electronic Maps to Analyze Structural Diversity in Bordetella pertussis Outbreak Strains

Despite increased administration of pertussis-containing vaccines, whooping cough cases in the United States and developing countries continue to rise. Recent publication of complete B. pertussis genomes from multiple outbreak events has revealed striking variation at the structural level between modern strain genomes and references used in vaccine development. Characterization of these structural variations through whole genome electronic mapping provides a comprehensive, high-resolution view of these changes that holds the potential for uncovering mechanisms of pathogenicity and vaccine evasion.

Nabsys has developed HD-Mapping™, a platform for the construction of electronic whole genome maps. The major advantages of electronic detection over optical methods are higher sensitivity, accuracy, scalability, and speed of detection, as well as greatly reduced cost. By analyzing single-molecule reads that are hundreds of kilobases in length, electronic detection preserves long-range information while simultaneously achieving unparalleled resolution and accuracy with low false-negative and false-positive error rates resulting in high information content per read. This allows the use of high-density nicking enzymes to generate complete and contiguous de novo assemblies.

Here we present the utilization of Nabsys HD-Mapping to generate de novo assembled HD maps of B. pertussis for the characterization of modern epidemic strain structural variation. As an illustration of the precision and accuracy of Nabsys HD-Mapping we compare our de novo assembled HD maps to completed references. The assembled maps highlight the structural diversity present between strains within a single outbreak. Furthermore, we demonstrate the ability to resolve a complex, nested repeat structure that spans hundreds of kilobases that was previously unresolved using PacBio, Illumina, and optical mapping data. The generation of dense, highly accurate whole genome electronic maps of pathogenic strains, such as B. pertussis, enables a level of structural analysis unavailable using existing sequencing and mapping technologies.