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

How to get started
Protocol and quality assessment
Tools and software
Benchmarking
Inter-EURLs Working Group on NGS
Upload to European Nucleotide Archive (ENA), ENA private hubs, and assessing data
E-learning
Proficiency test
Companies for outsourcing
Recommended publications
Useful links

1. How to get started

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:

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

WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) has published a document that addresses the applications of WGS for AMR surveillance, including the benefits and limitations of current WGS technologies. It can be found via the following link:

GLASS whole-genome sequencing for surveillance of antimicrobial resistance

2. Protocol and quality assessment

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

Protocol for whole genome sequencing and bioinformatics analysis of bacterial isolates related to the EU monitoring of antimicrobial resistance - version 2.2 (December 2021)

(PDF document 600 KB)

3. Tools and software

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.

ENGAGE - List of online bioinformatics tools and software used for capacity building (status January 2018)
(PDF document, 800 KB)

4. Benchmarking

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.

5. Inter-EURLs Working Group on NGS

Please find further details and documents via this link.

6. Upload to European Nucleotide Archive (ENA), ENA private hubs, and assessing data

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.

Sharing sequence data to enable collective action agains AMR

(PDF document, 7.5 MB)

7. E-learning

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

8. Proficiency test

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.

9. Companies for outsourcing

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 (in alphabetical order):

AllGenetics

BGI, worldwide

Genohub Inc., Austin, USA

Genomed S.A., Warsaw, Poland

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.