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Newsletter #6 – Summer 2024

GenEpi-BioTrain Newsletter #6

Genomic Epidemiology and Public Health Bioinformatics Training in the EU/EEA,

the Western Balkans, and Türkiye

In this quarterly edition of the GenEpi-BioTrain newsletter, we are excited to present

the outcome of the most recent training initiatives and provide an overview of the

upcoming activities.

We are currently conducting training activities in Pathogen Wave 2 (Antimicrobial

Resistance, AMR), Pathogen Wave 3 (Food and Waterborne Diseases, FWD) and

Pathogen Wave 4 (Vaccine-Preventable Infections, VPI).

A call for nominations for Pathogen Wave 5 (Tuberculosis, TB) and

Pathogen Wave 6 (AMR) will be launched in Q4 2024.

Our unwavering commitment is to provide an exceptional learning experience for all

nominated candidates within public health institutions.

Stay informed and engaged with GenEpi-BioTrain!

Two one-week exchange visits took place at Statens Serum Institut (SSI) in Denmark

in Q1 and Q2 2024.

The first visit was part of the activities for Block 1/Pathogen Wave 2 (AMR)

trainees and was held from 18th to 22nd March 2024.

GenEpi-BioTrain Month 1-18 (of 48)

✓ 83 face-to-face course days

• 185 trainees

▪ Nearly all EU/EEA countries represented

✓ 7 one-day virtual trainings:

• Ca. 2,000 registrations

▪ EU/EEA and other countries

1-week exchange visits for bioinformaticians

2

The second visit was part of the activities for Block 1/Pathogen Wave 3 (FWD)

trainees and was held from 15th to 19th April 2024.

Each visit was attended by five trainees from different EU/EEA countries.

The visits were tailored to meet individual trainees’ learning goals, which were

discussed among trainees, trainers and ECDC ahead of the visits.

The exchange visits revolved around three key themes, which were tackled at different

proficiency levels depending on the expertise of each trainee:

1. Command-line skills and workflow management: The course bolstered

the command-line expertise of trainees and deepened their understanding of

workflow management systems, particularly relevant for establishing robust

sequencing pipelines.

2. Phylogenetic Analysis and Visualization: Trainees harnessed tools to

create and visualize phylogenetic trees, enabling them to identify clusters and

suspected outbreaks.

3. Genomic surveillance: Trainees immersed themselves in studying the

pathogens in focus in the respective pathogen waves, acquired proficiency in

utilizing tools to detect AMR and discussed the role of plasmids in outbreak

detection and phylogenetic analysis.

These exchange visits also facilitated networking among participants and trainers

from SSI, fostering valuable connections for future collaboration.

It is expected that trainees will disseminate the knowledge gained during the exchange

visits with colleagues in their respective countries.

A three-day workshop was conducted as

part of Block 3/Pathogen Wave 3

(FWD) activities at the Institut Pasteur

(IP) in France from 22nd to 24th April 2024.

The workshop aimed to explore

evolutionary relationships between

organisms based on their genomes.

Participants gained insights into the

rationale behind phylogenetic analysis and

acquired practical skills to perform,

analyze, and interpret phylogenetic trees.

3-day workshop on Phylogeny

3

The workshop was focused on the following themes:

1) Finding the best evolutionary model for maximum likelihood analysis.

2) Inferring the phylogenetic tree results.

3) Assessing the clock signal in phylogenetic data and time scaling a phylogenetic tree.

4) Displaying, manipulating, and interpreting phylogenetic trees.

At the end of the course, trainees learned how to apply phylogenetic tools and methods

for real-time surveillance of FWD pathogens (Listeria monocytogenes, Salmonella

enterica, Escherichia coli, and Shigella species) and to convey the results to the

microbiologists and epidemiologists for surveillance and outbreak investigations.

Detailed information about this workshop can be found on EVA: Course: GenEpi-

BioTrain - Topical training: Phylogeny for food- and waterborne diseases (europa.eu).

A 3-day workshop was held at the Staten Serum

Institut (SSI) in Denmark as part of Block

1/Pathogen Wave 3 (FWD) and 4 (VPI)

activities from 14th to 16th May 2024.

This course was intended for beginners in

bioinformatics without prior knowledge of

Structured Query Language (SQL).

The course introduced SQL, its functionality, and its uses in public health surveillance.

This was the second edition of this workshop, which incorporated valuable feedback

from participants of the first edition to enhance the learning outcomes.

The workshop centered around the following key themes:

1. Data Manipulation: Participants learned effective techniques for

manipulating extensive data, including creating, joining, and altering tables.

2. Advanced SQL Skills: The workshop provided practical guidance on efficient

searching within SQL databases and applying functions to perform complex

tasks.

3. Automated Processes: Trainees also acquired the skills necessary to create

procedures for automating SQL processes.

By the conclusion of the course, participants gained comprehensive knowledge about

the utility of SQL databases and how to effectively manage data.

3-day workshop on SQL databases

4

Detailed information about this workshop can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Topical training: SQL for beginners 2024

(europa.eu).

A 2-week Interdisciplinary workshop on

genomic epidemiology and public health

bioinformatics was held at IP for Block

2/Pathogen Wave 3 (FWD) trainees

from 27th May to 7th June 2024.

The curriculum delved into surveillance

and outbreak investigation techniques

focusing on L. monocytogenes, S.

enterica, and E. coli, with additional

considerations related to Klebsiella

pneumoniae and Campylobacter jejuni.

This workshop brought together thirty participants from ten EU/EEA countries,

representing collaborative country teams of epidemiologists, microbiologists and

bioinformaticians to explore how interdisciplinary interpretation of integrated results

can enhance efforts to effectively prevent and control the spread of infectious diseases.

The workshop focused on several key themes:

1. Enhanced Understanding of Genomic Epidemiology and

Bioinformatics: Participants developed a deeper grasp of genomic

epidemiology and bioinformatics, equipping them with essential knowledge for

analyzing genetic data in public health contexts.

2. Proficiency in Open-Source Tools: Trainees honed their skills in utilizing

open-source tools for integrated analysis and visualization of genomic and

epidemiological data. This practical training aimed to empower them with the

necessary tools to address real-world challenges.

3. Promoting Collaboration: The workshop fostered collaboration among

epidemiologists, microbiologists, and bioinformaticians within public health

institutions. By enhancing teamwork and effectiveness, this collaborative

approach contributes to more robust surveillance and response strategies.

2-week Interdisciplinary workshop

5

Feedback from trainees indicated that the workshop significantly improved their

competencies, enabling them to effectively handle actual public health genomic

surveillance of FWD.

For detailed information about this workshop, please refer to EVA: Course:

GenEpi-BioTrain - Interdisciplinary training in genomic epidemiology and public

health bioinformatics on food- and waterborne diseases (europa.eu).

Future activities are presented in chronological order.

IP will organize a Virtual Training titled “Waterborne disease (Leptospirosis)

and Water Surveillance”. The training will take place on 22nd & 24th July 2024.

Over 150 participants have already registered for the course on the EVA platform and

registration is still open.

The primary focus of this training is to introduce participants to both theoretical and

practical aspects of waterborne disease surveillance, using Leptospirosis as a specific

example. For detailed information about this workshop and for registration, please

visit the EVA platform.

Course: GenEpi-BioTrain - Virtual training 8 - Waterborne disease and Water

Surveillance (europa.eu).

SSI will organize a Virtual Training titled “Unix for beginners & Introduction

to the Conda ecosystem”. The training will take place on 20th, 21st, and 22nd

August 2024.

The webinar aims at providing a general introduction to working in Unix (i.e. use the

command-line) as well as creating Conda environments for running simple

bioinformatics tasks. In preparation of this webinars, trainees will receive detailed

instructions to prepare themselves to work in a Unix ecosystem. A dedicated course

space with all details will be open on EVA at the beginning of August 2024.

A two-week exchange visit for bioinformaticians will be conducted at SSI from

26th August to 6th September 2024 for five trainees belonging to pathogen wave two

i.e., AMR. The program centers around analyses of trainees’ own data and is

customized to meet individual trainees’ needs and align with GenEpi-BioTrain goals.

Additional training activities are planned for Q4 2024 and will be communicated in

the next newsletter.

Upcoming activities

1

Newsletter #6 – Summer 2024

GenEpi-BioTrain Newsletter #6

Genomic Epidemiology and Public Health Bioinformatics Training in the EU/EEA,

the Western Balkans, and Türkiye

In this quarterly edition of the GenEpi-BioTrain newsletter, we are excited to present

the outcome of the most recent training initiatives and provide an overview of the

upcoming activities.

We are currently conducting training activities in Pathogen Wave 2 (Antimicrobial

Resistance, AMR), Pathogen Wave 3 (Food and Waterborne Diseases, FWD) and

Pathogen Wave 4 (Vaccine-Preventable Infections, VPI).

A call for nominations for Pathogen Wave 5 (Tuberculosis, TB) and

Pathogen Wave 6 (AMR) will be launched in Q4 2024.

Our unwavering commitment is to provide an exceptional learning experience for all

nominated candidates within public health institutions.

Stay informed and engaged with GenEpi-BioTrain!

Two one-week exchange visits took place at Statens Serum Institut (SSI) in Denmark

in Q1 and Q2 2024.

The first visit was part of the activities for Block 1/Pathogen Wave 2 (AMR)

trainees and was held from 18th to 22nd March 2024.

GenEpi-BioTrain Month 1-18 (of 48)

✓ 83 face-to-face course days

• 185 trainees

▪ Nearly all EU/EEA countries represented

✓ 7 one-day virtual trainings:

• Ca. 2,000 registrations

▪ EU/EEA and other countries

1-week exchange visits for bioinformaticians

2

The second visit was part of the activities for Block 1/Pathogen Wave 3 (FWD)

trainees and was held from 15th to 19th April 2024.

Each visit was attended by five trainees from different EU/EEA countries.

The visits were tailored to meet individual trainees’ learning goals, which were

discussed among trainees, trainers and ECDC ahead of the visits.

The exchange visits revolved around three key themes, which were tackled at different

proficiency levels depending on the expertise of each trainee:

1. Command-line skills and workflow management: The course bolstered

the command-line expertise of trainees and deepened their understanding of

workflow management systems, particularly relevant for establishing robust

sequencing pipelines.

2. Phylogenetic Analysis and Visualization: Trainees harnessed tools to

create and visualize phylogenetic trees, enabling them to identify clusters and

suspected outbreaks.

3. Genomic surveillance: Trainees immersed themselves in studying the

pathogens in focus in the respective pathogen waves, acquired proficiency in

utilizing tools to detect AMR and discussed the role of plasmids in outbreak

detection and phylogenetic analysis.

These exchange visits also facilitated networking among participants and trainers

from SSI, fostering valuable connections for future collaboration.

It is expected that trainees will disseminate the knowledge gained during the exchange

visits with colleagues in their respective countries.

A three-day workshop was conducted as

part of Block 3/Pathogen Wave 3

(FWD) activities at the Institut Pasteur

(IP) in France from 22nd to 24th April 2024.

The workshop aimed to explore

evolutionary relationships between

organisms based on their genomes.

Participants gained insights into the

rationale behind phylogenetic analysis and

acquired practical skills to perform,

analyze, and interpret phylogenetic trees.

3-day workshop on Phylogeny

3

The workshop was focused on the following themes:

1) Finding the best evolutionary model for maximum likelihood analysis.

2) Inferring the phylogenetic tree results.

3) Assessing the clock signal in phylogenetic data and time scaling a phylogenetic tree.

4) Displaying, manipulating, and interpreting phylogenetic trees.

At the end of the course, trainees learned how to apply phylogenetic tools and methods

for real-time surveillance of FWD pathogens (Listeria monocytogenes, Salmonella

enterica, Escherichia coli, and Shigella species) and to convey the results to the

microbiologists and epidemiologists for surveillance and outbreak investigations.

Detailed information about this workshop can be found on EVA: Course: GenEpi-

BioTrain - Topical training: Phylogeny for food- and waterborne diseases (europa.eu).

A 3-day workshop was held at the Staten Serum

Institut (SSI) in Denmark as part of Block

1/Pathogen Wave 3 (FWD) and 4 (VPI)

activities from 14th to 16th May 2024.

This course was intended for beginners in

bioinformatics without prior knowledge of

Structured Query Language (SQL).

The course introduced SQL, its functionality, and its uses in public health surveillance.

This was the second edition of this workshop, which incorporated valuable feedback

from participants of the first edition to enhance the learning outcomes.

The workshop centered around the following key themes:

1. Data Manipulation: Participants learned effective techniques for

manipulating extensive data, including creating, joining, and altering tables.

2. Advanced SQL Skills: The workshop provided practical guidance on efficient

searching within SQL databases and applying functions to perform complex

tasks.

3. Automated Processes: Trainees also acquired the skills necessary to create

procedures for automating SQL processes.

By the conclusion of the course, participants gained comprehensive knowledge about

the utility of SQL databases and how to effectively manage data.

3-day workshop on SQL databases

4

Detailed information about this workshop can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Topical training: SQL for beginners 2024

(europa.eu).

A 2-week Interdisciplinary workshop on

genomic epidemiology and public health

bioinformatics was held at IP for Block

2/Pathogen Wave 3 (FWD) trainees

from 27th May to 7th June 2024.

The curriculum delved into surveillance

and outbreak investigation techniques

focusing on L. monocytogenes, S.

enterica, and E. coli, with additional

considerations related to Klebsiella

pneumoniae and Campylobacter jejuni.

This workshop brought together thirty participants from ten EU/EEA countries,

representing collaborative country teams of epidemiologists, microbiologists and

bioinformaticians to explore how interdisciplinary interpretation of integrated results

can enhance efforts to effectively prevent and control the spread of infectious diseases.

The workshop focused on several key themes:

1. Enhanced Understanding of Genomic Epidemiology and

Bioinformatics: Participants developed a deeper grasp of genomic

epidemiology and bioinformatics, equipping them with essential knowledge for

analyzing genetic data in public health contexts.

2. Proficiency in Open-Source Tools: Trainees honed their skills in utilizing

open-source tools for integrated analysis and visualization of genomic and

epidemiological data. This practical training aimed to empower them with the

necessary tools to address real-world challenges.

3. Promoting Collaboration: The workshop fostered collaboration among

epidemiologists, microbiologists, and bioinformaticians within public health

institutions. By enhancing teamwork and effectiveness, this collaborative

approach contributes to more robust surveillance and response strategies.

2-week Interdisciplinary workshop

5

Feedback from trainees indicated that the workshop significantly improved their

competencies, enabling them to effectively handle actual public health genomic

surveillance of FWD.

For detailed information about this workshop, please refer to EVA: Course:

GenEpi-BioTrain - Interdisciplinary training in genomic epidemiology and public

health bioinformatics on food- and waterborne diseases (europa.eu).

Future activities are presented in chronological order.

IP will organize a Virtual Training titled “Waterborne disease (Leptospirosis)

and Water Surveillance”. The training will take place on 22nd & 24th July 2024.

Over 150 participants have already registered for the course on the EVA platform and

registration is still open.

The primary focus of this training is to introduce participants to both theoretical and

practical aspects of waterborne disease surveillance, using Leptospirosis as a specific

example. For detailed information about this workshop and for registration, please

visit the EVA platform.

Course: GenEpi-BioTrain - Virtual training 8 - Waterborne disease and Water

Surveillance (europa.eu).

SSI will organize a Virtual Training titled “Unix for beginners & Introduction

to the Conda ecosystem”. The training will take place on 20th, 21st, and 22nd

August 2024.

The webinar aims at providing a general introduction to working in Unix (i.e. use the

command-line) as well as creating Conda environments for running simple

bioinformatics tasks. In preparation of this webinars, trainees will receive detailed

instructions to prepare themselves to work in a Unix ecosystem. A dedicated course

space with all details will be open on EVA at the beginning of August 2024.

A two-week exchange visit for bioinformaticians will be conducted at SSI from

26th August to 6th September 2024 for five trainees belonging to pathogen wave two

i.e., AMR. The program centers around analyses of trainees’ own data and is

customized to meet individual trainees’ needs and align with GenEpi-BioTrain goals.

Additional training activities are planned for Q4 2024 and will be communicated in

the next newsletter.

Upcoming activities