Application of Genomic Tools –

One technology takes it all

Rene Hendriksen
 Outline
• Evolution in typing techniques

• The tool box of the Center for Genomic Epidemiology (CGE)

• A summary

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 Evolution of sub-typing technologies –
Memory lane!
IS-
typing flj-
RFLP typing
REA
PFGE VTNR
Plasmid MLEE
Phage profiles RAPD
typing AFLP
Bacteriocin
Serotyping typing

1920 1940 1960 1970 1980 2000

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Present and future typing …….What lies ahead?
MLST
AFLP Next Generation
Sequencing (NGS)
VTNR
Array

2000 2010 2015

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 Old School –
Current conventional bacterial diagnostics

Characterization / sub-typing
Sample Isolation Molecular typing
(Gram stain, spp/ ssp ID,
(Faeces etc.) (media) (PFGE etc.)
susceptibility test)

1 – 2 days 1 week > weeks

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 New School –
Culture based diagnostics using NGS

Sample DNA
Isolation Characterization
√ √ / sub-typing
√ √ Interpretation
(Faeces prep.
(media) Tool Tool Tool
(bioinformatics) Tool
etc.) NGS

1 – 2 days 2 – 3 days 1 – 12 hours 1 day

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Next Generation Sequencing (NGS)

- One technology takes it all!

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 The 100 mill. $$$$ question -
when will NGS replace all other techniques?

• Next Generation Sequencing – today between 50 € to 100 €

per genome or 10 €?

• Traditional typing techniques (costs at DTU Food):

– Identification – 10 €
– Serotyping – 40 €
– Susceptibility testing – 15 € to 25 €
– Pulsed-field gel electrophoresis (PFGE) – 50 €
– Multilocus sequence typing (MLST) – 250 €
– Molecular characterisation – 10 € to 1000 €
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 Preparing for Global Surveillance -
Center for Genomic Epidemiology (CGE)
• Provide a proof of concept of combining bioinformatics with global epidemiology
in real-time (2010-2016)

• Provide foundation for web based solutions (plug and play tool)
– Rapid sequence assembly and annotation
• What is it (species)
• How dangerous is it (virulence)
• Have we seen it before (phylogeny)
• With what can it be treated (resistance)

• www.genomicepidemiology.org

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 CGE development of bioinformatic pipelines
for identification of epidemiological markers
Isolation
Campylobacter DNA prep √ √
Isolation Characterization / sub-typing Interpretation
Tool Tool
NGS
Isolation Bioinformatic
√
E. coli Isolation
DNA prep plugToolandToolplay
√
Characterization / sub-typing Interpretation
NGS
Isolation tools
√ √ √ √
Salmonella Isolation
DNA prep Characterization / sub-typing Interpretation
Tool Tool Tool Tool
NGS

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 Overview of CGE tools

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http://cge.cbs.dtu.dk/services/all.php - Firefox browser Module1
 Other applications and diagnostic use

• Human genomics
• Cancer genetics
• Personalized medicine
• Functional genomics
• Structural genomics
• Metagenomics
• Viruses and bacteriophages
• Bioengineering
• Etc.…..

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 In summary

• Using Next Generation Sequencing (NGS) reduced the time

tremendously for the analysis – down to only 5 days from
sample to sequencing results!

• NGS has advanced – analytic NGS tools are available

providing meaningful low cost and timely data incl. detection
of antimicrobial resistance gene
– A need for more to provide plain language reports

• There is an urgent need for

– Standardization in all aspects – Quality Control
– Tool development
– Extend the usage of NGS
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 Thank you very much!

Rene S. Hendriksen, PhD

Research Group of Genomics Epidemiology

WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens and Genomics
European Union Reference Laboratory for Antimicrobial Resistance

National Food Institute, Technical University of Denmark

rshe@food.dtu.dk

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