Whole-genome sequencing in outbreak analysis

Abstract

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. 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.

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.

FIG 2

Conceptual representation of a microbial forensics bioinformatic pipeline. There are three components necessary for microbial forensic analysis with NGS data. First, a DNA sequence of the sample is needed (1), which could be a completed draft genome assembly, shotgun metagenomic sequences, or amplicon sequences such as 16S rRNA or protein-encoding genes. Algorithm/software implementation (2) is the necessary link between the sample sequence data (1) and a comprehensive reference database (3) consisting of all available draft and complete genomes, metagenomes, 16S rRNA gene sequences, or other protein-encoding gene sequences.