Overview of Next Generation Sequencing

During the last decade, the sequencing technology has evolved making it possible to sequence the full genome of a microorganism in a matter of hours at a cost that equals that of many other molecular methods used in the laboratory. At the same time the IT-infrastructure and bioinformatics disciplines have evolved making it possible to store, analyze, share and communicate the huge amounts of data generated. Next generation sequencing is based on the principle of massive parallel sequencing where the genome is sequenced multiple times in random small pieces which subsequently are assembled and analyzed using bioinformatics software. The technology is increasingly used in academia and is transforming microbiology in many public health and food regulatory laboratories by replacing many of the traditional phenotypic and molecular methods currently in use. A number of characteristics of a microorganism can be directly be predicted from its sequence, e.g., its genus and species, serotype, virulence profile and resistance to antimicrobials and disinfectants. Whole genome sequencing has also proven to have superior discrimination and precision compared to other subtyping methods, e.g., PFGE. This makes the method almost ideal for source tracking and to study transmission chains in a food production facility. For this reason it is also being adopted by food industry laboratories. Currently, the technology is mainly used to characterize microorganisms in pure culture but it is increasingly also being used to characterize complex populations of microorganisms in clinical and food samples (metagenomics).