24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.

1. GERMANFEDERALINSTITUTE
FORRISKASSESSMENT
Activities in development of bioinformatics pipelines
for characterisation of foodborne pathogens
Simon Tausch

2. Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides page 2
What do we do at the Federal Institute for Risk Assessment?

3. page 3Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Foodborne pathogens in Germany- reported human cases 2000-2018

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Foodborne Outbreaks in Germany - 2017
• In total: 875 potential foodborne outbreaks
with 2777 disease cases
• 316 outbreaks were classified as
„explicit foodborne“
🡪🡪 1375 disease cases
🡪🡪 2 death cases
+ 19 explicit foodborne
Norovirus-gastroenteritis outbreaks
with 68 cases
• Causative agents:
Robert Koch-Institut. Infektionsepidemiologisches Jahrbuch meldepflichtiger Krankheiten für 2017, Berlin 2018
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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Establishing integrated genomic outbreak investigation in Germany
universal approach
high-throughput
increased information output
Improvement of pathogen
surveillance and outbreak
investigation
data exchangeability
and comparability
cost & work efficiency
funding
harmonization & standardization
Establishment of common
databases, nomenclature systems
and data sharing
Communication and interpretation
of results
Convince people to phase out old
methods
Challenges Chances
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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Who are we?
• Study Centre for Genome Sequencing and Analysis
• Part of Department Biological Safety
• Translate cutting edge tech into everyday regulatory use

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What do we do at the Federal Institute for Risk Assessment?
• Official duties: Help national reference laboratories with
○ Sequencing
○ Data analysis
○ Pathogen surveillance
○ Outbreak analysis
○ Conceptualization and implementation of workflows
○ Implementation of new technologies
○ Training

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And besides that?
• Research projects:
○ Tool development
○ Data analysis for research projects
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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Wet-lab setup
Oxford Nanopore MinIon Pacbio Sequel Thermo Scientific
PGM
Illumina MiSeq Illumina NextSeq
Throughput 15-30 Gbp 1-10 Gbp 2 Gbp 15Gbp 120Gbp
Runtime < 48 h < 20 h 2-7 h 48-62 h 29 h
Read length < 700 kbp < 175 kbp ~400 bp 2*200-2*300 bp 2*150 bp
Base quality - ++ + +++ +++
USP Easiest prep Full high quality enomes Least contamination Flexible, high quality Best bang for the buck
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

10. page 10Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Sequencing activities

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Drylab methods and capacities
Core services: Reward bioinformaticians (Jeffrey Chang, Nature 520, 151–152 (09 April 2015) doi:10.1038/520151a) Source: Univ. Texas Health Science Center
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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FlexibililtyReproducibility
Throughput/
Frequency
Automatization
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Drylab methods and capacities

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Quality Check
Assembly
AMR genes
Gene database search
SNP calling
cgMLST profiling
FlexibililtyReproducibility
Throughput/
Frequency
Automatization
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Drylab methods and capacities

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Quality Check
Assembly
AMR genes
Gene database search
SNP calling
cgMLST profiling
FlexibililtyReproducibility
Throughput/
Frequency
Automatization
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Understand reports
and metrics
In-depth analysis of result files
Pipelines
Drylab methods and capacities

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Quality Check
Assembly
AMR genes
Gene database search
SNP calling
cgMLST profiling
Taxonomic classification
Search individual gene
Comparison to
external data
Compare different assembly methods
Gene neighborhood analysis
Visual inspection of genomic structure
FlexibililtyReproducibility
Throughput/
Frequency
Pathway analysis
Automatization
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Understand reports
and metrics
In-depth analysis of result files
Pipelines
Drylab methods and capacities

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Quality Check
Assembly
AMR genes
Gene database search
SNP calling
cgMLST profiling
Taxonomic classification
Search individual gene
Comparison to
external data
Compare different assembly methods
Gene neighborhood analysis
Visual inspection of genomic structure
Understand reports
and metrics
In-depth analysis of result files
Linux command line
Geneious / Bionumerics
FlexibililtyReproducibility
Throughput/
Frequency
Pathway analysis
Automatization
Pipelines
Scripts/
comands
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
Drylab methods and capacities

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Workflows - AQUAMIS
Assembly Based QUality Assessment for Microbial Isolate Sequencing
Snakemake pipeline based on:
- Read trimming: fastp
- Assembly: Unicycler
- Assembly evaluation: QUAST
- Reference search: mash
Aim:
- Fully automated basic analysis and quality control
- Comprehensible metrics, yet detailed insights
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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Workflows - BacCharac
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides
BACterial CHARACterization
Snakemake pipeline based on:
- Resistence/virulence gene search: abricate
- Plasmid search: BLAST
- Annotation: PROKKA
- Reference search: mash
- MLST typing: mlst against pubmed 7 gene database
Aim:
- More detailed species specific analysis

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Search for novel genes
- Newly discovered colistin resistance gene MCR9
- Found in:
1 Enterobacter
32 Escherichia
86 Salmonella
N50[bp]
Usecases
Sequencing kit evaluation
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

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Conclusion
● The German Federal Institute for Risk Assessment is involved in following activities:
• There is a transition in Germany to investigate outbreaks using WGS technologies
-> WGS is implemented in food safety authorities on national and federal state level
• Standardization and harmonization of data generation and metadata nomenclature is
needed to ensure data comparability
-> national working groups are created
• Accreditation of data generation and analysis is necessary before WGS can replace
standard methods
• Need in rethinking: open data & open access
Simon Tausch, 24 June 2019, Bioinformatics and regulation of microbial pesticides

26. GERMANFEDERALINSTITUTE
FORRISKASSESSMENT
Thank you for your attention
German Federal Institute for Risk Assessment
Max-Dohrn-Str. 8-10 ● 10589 Berlin, GERMANY
Phone +49 30 - 184 12 - 0 ● Fax +49 30 - 184 12 – 99 0 99
bfr@bfr.bund.de ● www.bfr.bund.de/en