Infokiri

1

Newsletter #5 – Spring 2024

GenEpi-BioTrain

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

Western Balkan, and Türkiye

Dive into the forefront of various training activities in this quarterly edition of the GenEpi-

BioTrain newsletter, where we strive to provide the best learning experience to all the

nominated candidates working in public health institutions.

In this newsletter, join us as we unravel various training activities that have already been

conducted and planned for the first and second quarters of 2024.

A 3-day workshop was held at the Statens

Serum Institut (SSI), Denmark, from the 31st

to the 1st of February 2024, to enable the

trainees to perform whole genome

sequencing (WGS) based surveillance and

outbreak investigations of: methicillin-

resistant Staphylococcus aureus (MRSA),

carbapenem-resistant Enterobacterales

(CRE) and Clostridioides difficile.

This workshop was part of block three

training on pathogen wave two and was

attended by ten trainees from different

European countries. Most of the trainees

were bioinformaticians with different

proficiency levels.

The course introduced the utility of WGS

data for surveillance and outbreak

investigations of hospital-acquired infections caused by MRSA, CRE, and C. difficile. The

emphasis was on solving simulation exercises, supplemented with expert lectures routinely

using WGS in public health. The trainees enjoyed the training sessions and expressed their

satisfaction regarding the content, format, and teaching provided by the trainers during the

workshop. The presentation given by trainees about the bioinformatic pipeline in their own

“3-day workshop” on AMR

2

country provided valuable information about the current status of bioinformatic skills. It

further opened the possibility for networking among the countries.

At the end of the course, trainees learned how to use bioinformatic approaches to extract

information from the sequencing data and to convey it to microbiologists and epidemiologists

for surveillance and outbreak investigations. Detailed information about this workshop can

be found on ECDC Virtual Academy (EVA): Course: GenEpi-BioTrain - Topical training:

Bioinformaticians’ roles and responsibilities in WGS-based MRSA, CRE and Clostridioides

difficile surveillance and outbreak investigation (europa.eu)

“Interdisciplinary workshop”

A 2-week “Bridging the Gaps in

Bioinformatics” workshop was held at the

Staten Serum Institut (SSI), Denmark,

from 26 February to 8 March 2024, with

the overall objective of strengthening the

programming skills & knowledge,

database management, and supporting

development and usage of bioinformatic

tools in the public health context.

Ten trainees from different European

countries were selected for the course. This

workshop was part of block one training on

pathogen waves three and four. The trainees

had diverse professional backgrounds, such

as microbiologists and public health

specialists. Still, they had a common goal of learning the basics of bioinformatics to enable

them to work independently as bioinformaticians in their own country.

The workshop was organized into three main themes: a) processing and quality control of the

sequencing data to write a basic script using Python/bash, allowing them to extract information

from the processed data; b) developing a pipeline for generating a genome assembly, and 3)

finally to understand the underlying principle of good coding practice, code documentation,

etc. The workshop was mainly focused on hands-on exercises so the trainees could understand

the basics of coding practices and, later, apply the learned tools to generate a pipeline for

genome assembly by using raw reads as input. After completing the course, the trainees were

confident to perform fundamental analyses supporting epidemiological investigations,

including interaction with public databases. Detailed information about this workshop can be

Bridging the Gaps in Bioinformatics

iIibioinformatics”hvhvhfejgBBioinformatics

Bio

3

found on ECDC Virtual Academy (EVA): Course: GenEpi-BioTrain Training in Genomic

Epidemiology and Public Health Bioinformatics “Bridging the Gap” - Second edition (FWD

and VPD) (europa.eu)

Bridging the Gaps in Bioinformatics is one of the most sought-after courses among the various

training courses provided under the GenEpi-Biotrain program. The trainees on this course are

grouped as block one candidates, and they will further attend a one-week exchange visit and a

3-day Structured Query Language (SQL) course for beginners. At the end of the course,

participants’ feedback was collected as displayed as a graph below.

1. How would you rank this course overall? (10 is a perfect score)

2. Would you recommend this course to other people in your network?

4

The GenEpi-BioTrain team is hosting a series of virtual training sessions to attract the attention

of participants from diverse backgrounds. As the topics covered during the virtual training are

not limited to pathogen waves, a wide array of topics could be included depending on the

demands of the participants. Generally, one training is organized monthly, a recording of which

is available on the EVA platform and can be accessed even after the training is completed.

SSI organized the sixth virtual training on

“Introduction to SARS-CoV-2 wastewater

analysis” on 24th and 31st January 2024,

12:30-16:00 CET. In total, 378 participants

enrolled for the course on the EVA platform.

This virtual training introduced the concept

of wastewater surveillance and explained the

practical details of SARS-CoV-2 sample

preparation from wastewater for sequencing

and further analysis. Participants gained

insight into the analysis steps, such as

investigating lineage abundance from

sequencing data using command line tools.

Detailed information about this workshop

can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Virtual training 06: Introduction to SARS-CoV-2

wastewater analysis (europa.eu)

SSI organized the next virtual training on the

topic of “Phylogenetics and alignments”. It

was held on 19th and 20th March 2024,

12:30-16:00 CET. More than 450

participants enrolled for the course on the

EVA platform. The focus was on generating

phylogenies using state-of-the-art tools for

alignments and phylogenetic inference.

Detailed information about this workshop

can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Virtual

training 07 - Phylogenetics and alignments

(europa.eu)

Virtual trainings

5

Overview of all GenEpi-BioTrain virtual trainings on EVA:

Course: GenEpi-BioTrain - Virtual training 01: Whole-genome sequencing-based (WGS)

detection of antimicrobial resistance (AMR) in bacteria (europa.eu)

Course: GenEpi-BioTrain - Virtual training 02: From sequencer to polished reads for bacteria

(europa.eu)

Course: GenEpi-BioTrain - Virtual Training 03: Introduction to bioinformatic analysis of

SARS-CoV-2 amplicon sequencing data (europa.eu)

Course: GenEpi-BioTrain - Virtual training 04: Avian influenza NGS data analysis for

outbreak investigation from a one health perspective (europa.eu)

Course: GenEpi-BioTrain - Virtual training 05: Bacterial genome assembly and quality

control (europa.eu)

Course: GenEpi-BioTrain - Virtual training 06: Introduction to SARS-CoV-2 wastewater

analysis (europa.eu)

Course: GenEpi-BioTrain - Virtual training 07 - Phylogenetics and alignments (europa.eu)

Future activities are presented in chronological order.

An exchange visit for bioinformaticians is underway at SSI from 18th to 22nd March 2024

for the five trainees belonging to block one/pathogen wave two category who attended the

“Bridging the Gaps in Bioinformatics” workshop in May 2023. The exchange visits are

designed to cater to the individual needs of the trainees, and the agenda is based on the trainees'

preference to hone their skills for future needs in their own country.

An exchange visit for bioinformaticians will be conducted at SSI from 15th to 19th April

2024 for the five trainees belonging to block one/ pathogen wave three category who will also

attend the “Bridging the Gaps in Bioinformatics” workshop in February/March 2024. The

exchange visits are designed to cater to the individual needs of the trainees, and the agenda is

based on the trainees' preference to hone their skills for future needs in their own country.

A 3-day workshop on specific food- and water-borne diseases (FWD) topics will be held

at Institute Pasteur (IP), France, on 22nd – 24th April 2024 for ten block three trainees of

pathogen wave 3. This workshop will focus on conducting standard phylogenetic analyses in

the context of FWD surveillance and outbreak investigation.

Future activities

6

A 3-day workshop on “SQL databases” will be held at SSI on 14th – 16th May 2024 for

block one trainees of pathogen wave 3 (n=5) and pathogen wave 4 (n=5), who will also attend

the “Bridging the Gaps in Bioinformatics” workshop in February/March 2024. The course will

introduce SQL, its functionality, and its uses in public health surveillance.

A 2-week “Interdisciplinary genomic epidemiology and public health” workshop will be

held at IP from May 27th to June 7th, 2024, for block two / pathogen wave three trainees. It

will focus on Listeria monocytogenes, Salmonella enterica, and other foodborne pathogens,

including Escherichia coli and Klebsiella pneumoniae. The trainees will be introduced to

genomic epidemiology, bacterial population biology, bioinformatics concepts, and essential

tools for public health microbiology.

A two-week exchange visit for bioinformaticians will be conducted at SSI from 26th August

to 6th September 2024 for the five trainees belonging to the pathogen wave two/AMR

category. The exchange visits target bioinformaticians with some prior experience with WGS

data analysis. An announcement for the two-week exchange visit has been made, and the

potential candidates are encouraged to contact the National Focal Points (NFPs) of their

respective countries to apply for the spot.

Additional training activities will occur in 2024, and specific dates will be communicated in

the following newsletter.

1

Newsletter #5 – Spring 2024

GenEpi-BioTrain

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

Western Balkan, and Türkiye

Dive into the forefront of various training activities in this quarterly edition of the GenEpi-

BioTrain newsletter, where we strive to provide the best learning experience to all the

nominated candidates working in public health institutions.

In this newsletter, join us as we unravel various training activities that have already been

conducted and planned for the first and second quarters of 2024.

A 3-day workshop was held at the Statens

Serum Institut (SSI), Denmark, from the 31st

to the 1st of February 2024, to enable the

trainees to perform whole genome

sequencing (WGS) based surveillance and

outbreak investigations of: methicillin-

resistant Staphylococcus aureus (MRSA),

carbapenem-resistant Enterobacterales

(CRE) and Clostridioides difficile.

This workshop was part of block three

training on pathogen wave two and was

attended by ten trainees from different

European countries. Most of the trainees

were bioinformaticians with different

proficiency levels.

The course introduced the utility of WGS

data for surveillance and outbreak

investigations of hospital-acquired infections caused by MRSA, CRE, and C. difficile. The

emphasis was on solving simulation exercises, supplemented with expert lectures routinely

using WGS in public health. The trainees enjoyed the training sessions and expressed their

satisfaction regarding the content, format, and teaching provided by the trainers during the

workshop. The presentation given by trainees about the bioinformatic pipeline in their own

“3-day workshop” on AMR

2

country provided valuable information about the current status of bioinformatic skills. It

further opened the possibility for networking among the countries.

At the end of the course, trainees learned how to use bioinformatic approaches to extract

information from the sequencing data and to convey it to microbiologists and epidemiologists

for surveillance and outbreak investigations. Detailed information about this workshop can

be found on ECDC Virtual Academy (EVA): Course: GenEpi-BioTrain - Topical training:

Bioinformaticians’ roles and responsibilities in WGS-based MRSA, CRE and Clostridioides

difficile surveillance and outbreak investigation (europa.eu)

“Interdisciplinary workshop”

A 2-week “Bridging the Gaps in

Bioinformatics” workshop was held at the

Staten Serum Institut (SSI), Denmark,

from 26 February to 8 March 2024, with

the overall objective of strengthening the

programming skills & knowledge,

database management, and supporting

development and usage of bioinformatic

tools in the public health context.

Ten trainees from different European

countries were selected for the course. This

workshop was part of block one training on

pathogen waves three and four. The trainees

had diverse professional backgrounds, such

as microbiologists and public health

specialists. Still, they had a common goal of learning the basics of bioinformatics to enable

them to work independently as bioinformaticians in their own country.

The workshop was organized into three main themes: a) processing and quality control of the

sequencing data to write a basic script using Python/bash, allowing them to extract information

from the processed data; b) developing a pipeline for generating a genome assembly, and 3)

finally to understand the underlying principle of good coding practice, code documentation,

etc. The workshop was mainly focused on hands-on exercises so the trainees could understand

the basics of coding practices and, later, apply the learned tools to generate a pipeline for

genome assembly by using raw reads as input. After completing the course, the trainees were

confident to perform fundamental analyses supporting epidemiological investigations,

including interaction with public databases. Detailed information about this workshop can be

Bridging the Gaps in Bioinformatics

iIibioinformatics”hvhvhfejgBBioinformatics

Bio

3

found on ECDC Virtual Academy (EVA): Course: GenEpi-BioTrain Training in Genomic

Epidemiology and Public Health Bioinformatics “Bridging the Gap” - Second edition (FWD

and VPD) (europa.eu)

Bridging the Gaps in Bioinformatics is one of the most sought-after courses among the various

training courses provided under the GenEpi-Biotrain program. The trainees on this course are

grouped as block one candidates, and they will further attend a one-week exchange visit and a

3-day Structured Query Language (SQL) course for beginners. At the end of the course,

participants’ feedback was collected as displayed as a graph below.

1. How would you rank this course overall? (10 is a perfect score)

2. Would you recommend this course to other people in your network?

4

The GenEpi-BioTrain team is hosting a series of virtual training sessions to attract the attention

of participants from diverse backgrounds. As the topics covered during the virtual training are

not limited to pathogen waves, a wide array of topics could be included depending on the

demands of the participants. Generally, one training is organized monthly, a recording of which

is available on the EVA platform and can be accessed even after the training is completed.

SSI organized the sixth virtual training on

“Introduction to SARS-CoV-2 wastewater

analysis” on 24th and 31st January 2024,

12:30-16:00 CET. In total, 378 participants

enrolled for the course on the EVA platform.

This virtual training introduced the concept

of wastewater surveillance and explained the

practical details of SARS-CoV-2 sample

preparation from wastewater for sequencing

and further analysis. Participants gained

insight into the analysis steps, such as

investigating lineage abundance from

sequencing data using command line tools.

Detailed information about this workshop

can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Virtual training 06: Introduction to SARS-CoV-2

wastewater analysis (europa.eu)

SSI organized the next virtual training on the

topic of “Phylogenetics and alignments”. It

was held on 19th and 20th March 2024,

12:30-16:00 CET. More than 450

participants enrolled for the course on the

EVA platform. The focus was on generating

phylogenies using state-of-the-art tools for

alignments and phylogenetic inference.

Detailed information about this workshop

can be found on ECDC Virtual Academy

(EVA): Course: GenEpi-BioTrain - Virtual

training 07 - Phylogenetics and alignments

(europa.eu)

Virtual trainings

5

Overview of all GenEpi-BioTrain virtual trainings on EVA:

Course: GenEpi-BioTrain - Virtual training 01: Whole-genome sequencing-based (WGS)

detection of antimicrobial resistance (AMR) in bacteria (europa.eu)

Course: GenEpi-BioTrain - Virtual training 02: From sequencer to polished reads for bacteria

(europa.eu)

Course: GenEpi-BioTrain - Virtual Training 03: Introduction to bioinformatic analysis of

SARS-CoV-2 amplicon sequencing data (europa.eu)

Course: GenEpi-BioTrain - Virtual training 04: Avian influenza NGS data analysis for

outbreak investigation from a one health perspective (europa.eu)

Course: GenEpi-BioTrain - Virtual training 05: Bacterial genome assembly and quality

control (europa.eu)

Course: GenEpi-BioTrain - Virtual training 06: Introduction to SARS-CoV-2 wastewater

analysis (europa.eu)

Course: GenEpi-BioTrain - Virtual training 07 - Phylogenetics and alignments (europa.eu)

Future activities are presented in chronological order.

An exchange visit for bioinformaticians is underway at SSI from 18th to 22nd March 2024

for the five trainees belonging to block one/pathogen wave two category who attended the

“Bridging the Gaps in Bioinformatics” workshop in May 2023. The exchange visits are

designed to cater to the individual needs of the trainees, and the agenda is based on the trainees'

preference to hone their skills for future needs in their own country.

An exchange visit for bioinformaticians will be conducted at SSI from 15th to 19th April

2024 for the five trainees belonging to block one/ pathogen wave three category who will also

attend the “Bridging the Gaps in Bioinformatics” workshop in February/March 2024. The

exchange visits are designed to cater to the individual needs of the trainees, and the agenda is

based on the trainees' preference to hone their skills for future needs in their own country.

A 3-day workshop on specific food- and water-borne diseases (FWD) topics will be held

at Institute Pasteur (IP), France, on 22nd – 24th April 2024 for ten block three trainees of

pathogen wave 3. This workshop will focus on conducting standard phylogenetic analyses in

the context of FWD surveillance and outbreak investigation.

Future activities

6

A 3-day workshop on “SQL databases” will be held at SSI on 14th – 16th May 2024 for

block one trainees of pathogen wave 3 (n=5) and pathogen wave 4 (n=5), who will also attend

the “Bridging the Gaps in Bioinformatics” workshop in February/March 2024. The course will

introduce SQL, its functionality, and its uses in public health surveillance.

A 2-week “Interdisciplinary genomic epidemiology and public health” workshop will be

held at IP from May 27th to June 7th, 2024, for block two / pathogen wave three trainees. It

will focus on Listeria monocytogenes, Salmonella enterica, and other foodborne pathogens,

including Escherichia coli and Klebsiella pneumoniae. The trainees will be introduced to

genomic epidemiology, bacterial population biology, bioinformatics concepts, and essential

tools for public health microbiology.

A two-week exchange visit for bioinformaticians will be conducted at SSI from 26th August

to 6th September 2024 for the five trainees belonging to the pathogen wave two/AMR

category. The exchange visits target bioinformaticians with some prior experience with WGS

data analysis. An announcement for the two-week exchange visit has been made, and the

potential candidates are encouraged to contact the National Focal Points (NFPs) of their

respective countries to apply for the spot.

Additional training activities will occur in 2024, and specific dates will be communicated in

the following newsletter.