Whole Genome Sequencing

Application of whole genome sequencing (WGS) offers the possibility to rapidly transform and improve our understanding of the epidemiology of antimicrobial resistance (AMR) determinants. Below you find links to training material and publications, as well as more practical guidance and tools for performing WGS.

Please see below further details in relation to 

  1. How to get started
  2. Protocol and quality assessment
  3. Tools and software
  4. Benchmarking
  5. Inter-EURLs Working Group on NGS
  6. Upload to European Nucleotide Archive (ENA), ENA private hubs, and assessing data
  7. E-learning
  8. Proficiency test
  9. Companies for outsourcing
  10. Recommended publications
  11. Useful links

When starting up whole genome sequencing, several considerations are necessary about DNA extraction, library preparation, sequencing and data processing. You can find a guideline on how to get started here:

pdf_logo

ENGAGE Guideline on how to get started

(PDF document, 100 KB)

WHO has prepared a landscape paper that summarizes some of the benefits and challenges inherent in the implementation of WGS. It also provides an evidence base for some of the approaches to be considered in the guidance document. This landscape paper can be found via the following link:

Whole Genome Sequencing for foodborne disease surveillance - landscape paper

The use of WGS for prediction of resistance genes is not trivial, as it covers a range of different laboratory processes and bioinformatics applications, which can be performed in many different ways. Suggestions for commonly used technologies and methods within these areas are covered in the protocol below

One of the biggest obstacles for the implementation of WGS in laboratories is the absence of bioinformatics expertise to handle the vast amount of data. To cope with this, Center for Genomic Epidemiology (GGE) at the Technical University of Denmark was initiated in 2010. Basically, the aim of CGE is to provide tools and software that use WGS data for discovering the content of a sample (typing), predict its pathogenic potential, and which antimicrobials it might be resistant towards (phenotyping).

At the CGE homepage you can explore and use the many different webtools for free.

https://cge.cbs.dtu.dk/services/

Other online tools and software that can be used for processing whole genome sequencing data can be found in the document linked below.

Benchmarking exercises are important to assess the performance, and reliability of the available bioinformatics tools which have different complexity in design and function. The purpose of a benchmarking exercise is to assess the ability of the bioinformatics tool to provide reliable analysis of AMR gene content.

Please find information on recommended publications via this link.


Please find further details and documents via this link.

The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information. Provision of nucleotide sequence data to ENA or another International Nucleotide Sequence Database has become a central and mandatory step in the dissemination of research findings to the scientific community via published literature.

Here you find a presentation on how to upload data to ENA, about ENA private hubs and how to share and assess data through ENA private hub.

7. E-learning

Please follow this link to find e-learning courses on Antimicrobial Resistance, Whole Genome Sequencing and Metagenomics.

It is advisable for laboratories to participate in proficiency tests (PT) regarding WGS. This would represent an important tool for the evaluation and production of reliable laboratory results of consistently good quality within the area of DNA preparation, sequencing, and analysis (e.g. detection of AMR genes and detection of MLST).

Find further details about an example of a relevant PT via this link: DTU Genomic PT.

If performing whole genome sequencing is not possible in your laboratory facilities, there are several companies available world-wide to whom some or all of the sequencing and bioinformatics tasks can be outsourced. A list of some of the companies are provided here:

BGI, worldwide

Genomed S.A., Warsaw, Poland

Genohub Inc., Austin, USA 

Macrogen Europe, Amsterdam, Holland (order from Europe via til link: https://dna.macrogen-europe.com/eng/)

Novogene, worldwide

Oxford Genomics Centre, Oxford, United Kingdom

​Should you be familiar with other companies that offer sequencing and bioinformatics support we would be happy to include them on the list above. If so, please forward an email to suska@food.dtu.dk with information on the company name and website link.

Please find information on recommended publications via this link.

Find more information on WGS and AMR surveillance via these links:

Global surveillance of Antimicrobial Resistance

Global Microbial Identifier

WHO WGS portal

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