Question

Using an example, how has whole genome sequencing been used to determine outbreaks locally and internationally.

Answer 1

In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak.

FIG 1

Microbial forensics analysis diagram illustrating where NGS can fit within microbial forensic analysis. Legal considerations such as patient privacy and/or the rights of defendants/perpetrators are important to consider at the time of sample collection. WGS analysis requires both NGS and bioinformatic capacity. Legal requirements are also a factor in the possible uses of WGS information.

===>Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms.

===>If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed.

THE CASE FOR APPLYING WGS TO DETERMINE WHETHER AN OUTBREAK IS DUE TO DELIBERATE, ACCIDENTAL, OR NATURAL CAUSES:-

Genomic microbiology can give detailed information on biological samples, and the rapid advances in molecular technology allow WGS to be used as a routine investigatory tool. From a policy- and decision-making standpoint, it is critical to determine whether an outbreak is due to natural circumstances, an accidental release of a cultured or engineered organism, or a deliberate introduction of a known pathogenic organism. Under these circumstances, the ultimate goals are identification of the agent responsible for the outbreak and attribution of both its biological and geopolitical origins, with a high degree of certainty. The resultant information is central to making correct decisions that are required in response to the outbreak, such as whether a public health emergency should be declared, what scientific and legal mechanisms should be used to limit transmission and contain the outbreak, and even whether to trigger a response under the Biological and Toxin Weapons Convention (BTWC) .