Genome sequencing, diagnostic pathology, and ecology - the intersection of good science practice

Deep sequencing is a powerful tool that can be applied to samples to detect and even construct complete genomes of organisms that may be previously unidentified or unculturable. Another powerful tool for broad screening for... [ view full abstract ]

Deep sequencing is a powerful tool that can be applied to samples to detect and even construct complete genomes of organisms that may be previously unidentified or unculturable. Another powerful tool for broad screening for potential pathogens is consensus PCR, targeting broad viral, fungal or bacterial families and genera.
However, deep sequencing alone cannot provide biological context, association with disease, or the presence of lesions. Further characterization of the potential pathogen, along with determining the viability, virulence, pathophysiology, and transmissibility of the agent requires further study of the relationships between the host, potential pathogen, and the environment.
Case studies will be used to illustrate the limitations and strengths of each component of the diagnostic paradigm. Sequencing can identify organisms that are difficult or currently impossible to culture, but there are also cases of pathogen discovery when deep sequencing did not identify the pathogen. Or cases when sequencing or microbial isolation identified an agent that was not relevant to the disease, requiring an iterative process of information sharing between pathology and field information. The strengths of genome sequencing as an important tool in the discovery of potential reservoir hosts and emerging diseases will be outlined as well as the role it plays as an early warning system for the detection of new agents or the potential spread of an agent to populations at risk.
The presentation will end with a summary of the strengths of each component of the diagnostic process, and how they fit into the diverse and challenging new world order of disease emergence.