Next Generation Sequencing (NGS) is a technique to rapidly determine a complete or a specific part of a genome (i.e. the complete genetic composition of an organism), thanks to the parallel characterisation of multiple DNA sequences. This technique makes it also possible to rapidly recognise pathogens (i.e. the agents responsible for diseases such as bacteria, germs, etc.) via their genetic information. Hence it enables a more effective response to a wide range of communicable disease threats. Therefore, Sciensano has acquired this key technology in its laboratories and invested in the required computational infrastructure and expertise to timely manage, analyse and interpret the large datasets generated by NGS. This project has allowed to integrate state-of-the-art technologies such as NGS into both routine surveillance and emergency cases to support a proactive public health policy for the benefit of all citizens.
Next Generation Sequencing (NGS) technologies are expected to play a crucial role in pathogen surveillance and outbreak investigation with unprecedented potential for pathogen characterisation via its genetic information. While whole genome sequencing (WGS) has become commonly used for research purposes, its implementation in routine for pathogen characterisation in enforcement laboratories remains challenging. Firstly, the enforcement laboratories (NRLs, NRCs) need to acquire these key technologies and invest in the required computational infrastructure and expertise in bioinformatics to timely manage, analyse and interpret the generated large datasets. Secondly, when implementing any novel technology for routine purposes, harmonization criteria including method validation upon minimal performance criteria need to be considered, besides the initial development and optimization.
Therefore, in order to introduce NGS technologies in our public health practice and in particular in the enforcement laboratories, this project was kick-started by Sciensano.
Sequencing with a MiSEQ Illumina instrument
At the level of the wetlab, the biotech-platform of our Transversal activities in applied genomics (TAG) service has acquired a MiSEQ Illumina instrument. During this project, standard operational procedures were elaborated and extensively validated for the sequencing of Nextera XT prepared DNA libraries from a pathogen’s genomic content. As a result, all the obtained fastq-datasets are now validated against acceptance criteria for selected parameters at run and sample quality level and will be delivered in the course of 2019 to the Sciensano enforcement laboratories under accreditation ISO17025.
Creation of dedicated bioinformatics expertise and infrastructure
Additionally, the bioinformatics platform within our Transversal activities in applied genomics (TAG) service has recruited a staff of bioinformaticians and a software engineer in order to create the dedicated bioinformatics infrastructure and tools to analyse NGS data with a focus on user-friendly tools (push-button pipelines) to be used in routine by Sciensano’s enforcement laboratories. The pipelines are developed for the routine analysis of several isolated pathogens of interest (Neisseria meningitidis, Listeria monocytogenes, Escherichia coli, influenza, Mycobacterium tuberculosis, …) in order to provide a WGS-based alternative compared to conventionally used molecular typing and characterisation techniques. These pipelines use Illumina WGS data to perform various tasks such as automated quality control, de novo assembly, antimicrobial resistance characterization, and typing according to internationally employed schemes and standards, whilst performance criteria like repeatability, reproducibility and accuracy were also validated.
This project has demonstrated the added value and feasibility of employing WGS with the aim of being adapted to and integrated into routine use for both surveillance and emergency cases to support a proactive public health policy. This project had also facilitated the integration of Sciensano in new international networks and the development of new research project opportunities with internal and external funding.