We are now able to characterize completely closed microbial genomes using the third-generation, single molecule, real-time DNA sequencing on the Pacific Bioscience (PacBio) Sequencer. Currently, it is frequently challenging to correctly assemble bacterial genomes and plasmids from short reads, due to the frequency of repetitive regions. With long read technology, we can assemble, correctly, through large mobile elements such as phages, plasmids, insertion sequences, and pathogenicity islands. These enhanced sequencing capabilities provide a comprehensive view of genetic composition that allows the generation of: 1) high quality reference genomes for source tracking during a foodborne outbreak investigation, 2) understanding long-term evolution of foodborne pathogens, 3) new insights in drug resistance and transmission of mobile elements carrying antimicrobial resistance markers, and 4) information about the contribution of DNA modification on pathogenesis.

The benefits of using closed genomes in routine surveillance will be discussed. In this session, we are going to present examples where the use of closed genomes allowed answering diverse questions, which could not have been achieved using draft genomes generated by short reads technology. The use of closed genomes will allow the regulatory agencies and the food industry to gain a greater understanding of the genetic compositions of virulence genes, as well as antimicrobial resistance genes presence in these isolates; both targets being equally important when tracking and treating illnesses caused by these pathogenic organisms. Further, the availability of a fully closed reference genomes increases accuracy of clustering, which is needed to facilitate outbreak cluster detection and source tracking and to provide deeper insights into structural variations, which is critically important for public health.

Presentations