# SEARCHER WEBINAR ORGANIZATION 2025
# Promotion of PhD and Postdocs
## Suggested structure
- One main external speaker ECS
- 20 min talks
- One ECS SEARCHER speaker
- 20 min talk on broad general topic on SEARCHER
- Discussion for 20 minutes
- One more experienced SEARCHER member moderates the session
- Aiming to promote ECS from SEARCHER and oder ECS from external groups
- We will do two seminars in spring (April and May) and five in autumn (August, September, October, November, December)

## SEARCHER potential speakers
Anna Abramova
Marcus Wenne
Jorge Agramont
Yuselys Garcia Martinez
Faina Tskhay
Nicolas Gordon
Juan Inda Diaz
Ulrike Löber
Víctor Hugo Jarquín-Díaz

## Potential dates
Apr 2, 9, 23
May 21, 28
Aug 20, 27
Sep 17, 24
Oct 22, 29
Nov 12, 26
Dic 10

# SEARCHER WEBINAR ORGANIZATION 2024

## Suggested structure
- One main external speaker (long talk)
- 30 min talks
- One SEARCHER speaker (Short talk)
- 10 min talk on broad general topic on SEARCHER
- Discussion for 20 minutes
- ECS from the group moderates the session
- Aiming to promote SEARCHER work and get inside from external groups
- We will do two seminars in spring (April and May) and five in autumn (September (2), October, November, December)

## SEARCHER Speakers
Sofia K. Forslund
Thomas Berendonk
Luis Pedro Coelho
Rabaab Zahra
Etienne Ruppé
Johan Bengtsson-Palme
Emmanuel Nnadi
Uli Klümper
David Kneis

## (Proposed) External Speakers
#### Topic: ARG Transmission / Plasmids
Dr. Alvaro San Millan (PI) - Centro Nacional de Biotecnología – CSIC, Madrid - Plasmid Biology and Evolution
Dr. Jeronimo Rodríguez-Beltran (PI) - Ramón y Cajal University Hospital - Evolutionary dynamics of antibiotic resistance
Prof. Dr. A. Murat Eren (PI) - Plasmids, ARG cargo and functions to shape microbial ecosystems
Dr. Rachel Wheatley (PI Jr.) - Ecology and evolution of antibiotic resistance in bacterial pathogens
Prof. Dr. Craig MacLean (PI) - Resistance mobility and genomic driver of resistance
Dr. Alice Risely (Postdoc) - Host-plasmid network structure in wastewater is linked to antimicrobial resistance genes (Transmission)

#### Topic: ARG prediction / Computational approaches
Prof. Dr. Tommi Vatanen (PI) - Addressing antibiotic resistance: computational answers to a biological problem?
Dr. Natacha Couto (Postdoc) - Big data - ARGs, Antimicrobial susceptibility prediction from genomes
Prof. Bing Li (Tsinghua Uni, Shenzhen) – Metagenomic approaches to investigate environmental AMR
Dr. Katariina Pärnänen (Postdoc)- Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence
Laura May Murray (PhD student) - Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments
Prof. Erik Kristiansson (PI) – Latent antibiotic resistance gene diversity in human, animal, and environmental microbiomes

#### Topic: ARG Ecology and evolution / wildlife ARG
Prof.Dr. Peer Bork - Traversing European Coastlines: An expedition to study coastal ecosystems and their response to the environment, from molecules to communities
Prof. Dr. Katharina Schaufler (PI) - University of Greifswald - Epidemiology and ecology of antimicrobial resistance
Prof. Will Gaze (PI) - University of Exeter Medical School - Dissemination of AMR at a landscape scale and human exposure and transmission in aquatic environments
Dr. Marjon de Vos (Groningen Uni) – Antibiotic tolerance and microbial interactions in polymicrobial infections
Dr. Amelia Barber (PI Jr.) - Fungal communities and ARGs
Dr. Laura de Nies (Postdoc) - Evolution of the murine gut resistome following broad-spectrum antibiotic treatment
Wendy Figueroa (PhD student) - Impact of mutations in transcriptional regulators on antimicrobial resistance (UK-Cambridge)

#### Topic: Policy and communication
Dr. Stef Bronzwaer (EFSA European Food Safety Authority) - Policies for ARG monitoring in food
Dr. Eva Garmendia (Postdoc) -Impactful approaches for community-wide engagement on antibiotic resistance
Prof. Christian Munthe (University of Gothenburg) - Translating thoughts into actions: AMR ethical dilemmas
Malin Grape – Sweden's antibiotic resistance ambassador

### Spring seminars

- April 24 at 2:30 PM CET:
- Topic: **ARG Transmission**
- External speaker: Dr. Alvaro San Millan (PI)
- Affiliation:Centro Nacional de Biotecnología – CSIC, Madrid
- Talk: "Ecology and evolution of plasmid-mediated carbapenem resistance in a hospital"
- STATUS: **CONFIRMED**
- Contact: [e-mail]
- Twitter account:
- SEARCHER speaker: Uli Klümper ([e-mail])
- Talk: "Tracking rates and drivers of bacterial plasmid transfer"
- Moderator: Faina Tskhay ([e-mail])
- Registration link: https://mdc-berlin.zoom.us/webinar/register/WN_l4zmjaMRTkqeXsgOxe2-3Q
-
- May 22 at 2:00 PM CET:
- - Topic: **ARG Ecology and Evolution**
- External speaker: Prof. Dr. Katharina Schaufler (PI)
- Affiliation: Helmholtz Institute for One Health (HIOH) in Greifswald
- STATUS: **CONFIRMED**
- Contact: [e-mail]
- Twitter account:
- SEARCHER speaker: Emmanuel Nnadi Nnaemeka ([e-mail])
- Moderator: Víctor Hugo Jarquín-Díaz
- Registration link: https://mdc-berlin.zoom.us/webinar/register/WN_91tWFT1jSaSzlTGgBPM9Hg

##Links for presentation
http://antimicrobialresistance.eu/
http://antimicrobialresistance.eu/category/amr-digest/

### Autumn seminars

- October 15 (11 am):
- Topic: Special session **From EMBARK to SEARCHER**

EMBARK main outcomes seminar:

• Why to monitor AMR in the environment, how to implement it, and what is needed to succeed. (Bengtsson-Palme, 5-10 min)
• E. coli as an indicator for the surveillance of AMR in the environment (Berendonk, 10 min)
• Database and methodological biases affecting ARG analysis, including GMGC (Coelho, 10 min)
• ResFinderFG – Database and online platform for antibiotic resistance determinants identified through functional metagenomics (Ruppé/Gschwind, 10 min)
• Suggested antibiotic resistance genes to be targeted for monitoring based on qPCR studies. (Abramova, 10 min)
• Correspondence between qPCR and metagenomics for AMR monitoring (Löber/Jarquín-Díaz/Wenne, 10 min)
• AMR monitoring – where do we go from here (Panel Q&A 10-30 min)

Registration: https://mdc-berlin.zoom-x.de/meeting/register/u5MvdOygqD0uG9B7MywO89sFiS1WHLHj7D0N

EMBARK main outcomes seminar (December):

• A baseline for AMR in the environment (15 min)
• A framework for monitoring AMR in the environment (30 min)
• Recommended targets for AMR monitoring (ARGs etc.) (15 min)
• Implementation of the frameworks (15 min)
• Adaptations to low-resource settings (15 min)
• What’s next – proactive monitoring for future AMR threats (15 min)
• Q&A (15-30 min)

- External speaker: -
- Affiliation: -
- STATUS: -
- Contact: -
- Twitter account:
- EMBARK speaker(s):
- Johan Bengtsson-Palme
- Thomas Berendonk
- Sofia K. Forslund-Startceva / Luis Pedro Coelho
- Topics:
- Overview on how comparable different monitoringmethods are
- Monitoring framework
- Targets for monitoring
- Recommended bioinformatics methods
- Moderator:
- Registration link: should include a question to ask for workshop

- October 23:
- Topic: **Policy and communication**
- External speaker: Dr. Eva Garmendia (Project Coordinator)
- Affiliation: Uppsala Antibiotic Center
- STATUS: **CONFIRMED**
- Contact: [e-mail]
- Twitter account:
- SEARCHER speaker: Rabaab Zahra
- Moderator: Víctor Hugo Jarquín-Díaz
- Registration link: https://mdc-berlin.zoom-x.de/meeting/register/u5Moc-2tpj4pH90D0vlFjDMjWMCI9ZJIMJHR

- November 20:
- Topic: **ARG Transmission**
- External speaker: Dr. Rachel Wheatley (PI Jr.)
- Affiliation: School of Biological Sciences, Queen's University Belfast
- STATUS: **CONFIRMED**
- Contact: [e-mail] or [e-mail]
- Twitter account:
- SEARCHER speaker: David Kneis
- Moderator: Víctor Hugo Jarquín-Díaz
- Registration link:

- December 11:
- Topic: **ARG Prediction**
- External speaker: Prof. Dr. Tommi Vatanen (PI)
- Affiliation:
- STATUS: **CONFIRMED**
- Contact: [e-mail]
- Twitter account:
- SEARCHER speaker: Etienne Ruppé
- Moderator: Víctor Hugo Jarquín-Díaz
- Registration link:

# EMBARK WEBINAR ORGANIZATION 2023

## Suggested structure
- Two main speakers with same/similar topic
- External JPIAMR project speaker
- EMBARK speaker
- Each speaker with 20 min talks
- Discussion for 20 minutes
- Postdoc from the group moderates the session
- Aiming to promote EMBARK work and put it in the context of other JPIAMR projects
- Considering the N=6 from EMBARK groups, we could do three seminars in spring (April, May, June and three in autumn (September, October, November)

## Suggested dates, speakers and topics 2023
### Spring seminars
- April 19:
- Topic: AMR Surveillance in aquatic environments
- JPIAMR speaker: **Sabrina Giebner** (Project AquaticPollutantsTransNet)
- Affiliation: Dechema
- STATUS: **Confirmed**
- Contact: [e-mail]
- Aim of JPIAMR project: Improve stakeholders’ & citizens’ perception through active involvement in the reduction of aquatic pollutants in the water cycle
- Twitter account: @aquapollutants
- EMBARK speaker: **Thomas Berendonk**
- Moderator: **Victor Hugo Jarquin Diaz**
- Registration link: https://gu-se.zoom.us/webinar/register/WN_h8-CkMMeQpixgDQ8Jtz7Dg
- May 17:
- Topic: ARG annotation
- JPIAMR speaker: Andrew Stubbs (Project Seq4AMR)
- Contact: [e-mail],[e-mail],[e-mail]
- STATUS: **Confirmed**
- Aim of project: Establish a strategy to link AMR NGS stakeholders and individual fields of NGS technologies, algorithms, quality standards, teaching/training and sequence databanks
- EMBARK speaker: **Luis Pedro Coelho**
- Moderator: **Svetlana Ugarčina Perović**
- Registration link: https://gu-se.zoom.us/webinar/register/WN_L7QmrDM5Rn2sWRnC7FnhVQ
- June 14:
- Topic: Strategies for AMR surveillance with an One Health approach
- JPIAMR speaker: **Frank van Leth** (Project OASIS)
- Contact: [e-mail]
- STATUS:**Confirmed**
- Aim of project: Optimise the Lot Quality Assurance Sampling (LQAS) approach as a rapid, domain-, and setting-appropriate AMR surveillance strategy, within a One Health context
- EMBARK speaker: **Johan Bengtsson-Palme**
- Moderator: **Anna Abramova**
- Registration link: https://gu-se.zoom.us/webinar/register/WN_-XjYy26RTlWyWLWMFagyOw

### Autumn seminars
- September 13:
- Topic: Molecular and culture based methods for AMR survillance in aquatic environments and animals
- JPIAMR speaker: **Jonas Bonnedahl** (Project PAIRWISE)
- Contact: [e-mail]
- Aim of project: Advance knowledge of antimicrobial resistance (AMR) as a pollution in aquatic environments, wildlife, and livestock. PAIRWISE focuses on dispersal and dynamics of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARG) and antibiotics (ATB) in aquatic environments affected by wastewater treatment plants (WWTPs)
- EMBARK speaker: **Rabaab Zahra**
- Moderator: **Victor Hugo Jarquin Diaz**
- STATUS: Invitation sent
- October 11:
- Topic: AMR: a link between clinical settings and other environments
- JPIAMR speaker: **Adam Roberts** (Project STRESST)
- Contact: [e-mail]
- Aim of project: Determine if hospital wide antimicrobial stewardship implementation will reduce antibiotics and antibiotic resistant bacteria from entering the environment
- EMBARK speaker: **Etienne Ruppé**
- Moderator: **Rémi Gschwind**
- STATUS: **CONFIRMED**
- November 15:
- Topic: Ecology and evolution of ARGs: From surveillance to intervention strategies
- JPIAMR speaker: **Craig MacLean** (ProjectMOB-TARGET)
- Contact: [e-mail]
- Aim of project: Stablish a series of novel interventions based on phages to combat mobile resistance genes
- EMBARK speaker: **Sofia K. Forslund**
- Moderator: **Ulrike Löber**
- STATUS: **CONFIRMED**

## Other options
**JPIAMR projects**
- Specific Targeting of Antimicrobial Resistant Strains in situ using Targeted-Antibacterial-Plasmids (STARS-TAP)
- Developing an innovative non-antibiotic antibacterial methodology to specifically target AMR strains from natural bacterial communities in several ecosystems in situ
- Christian Lesterlin, Centre National de la Recherche Scientifique, France (Coordinator)

- DisPersal of AntIbiotic Resistance and antibiotics in Water ecosystems and Influence on liveStock and aquatic wildlife (PAIRWISE)
- Study dispersal and dynamics of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARG) and antibiotics (ATB) in aquatic environments affected by wastewater treatment plants (WWTPs)
- Anna Olsson, National Veterinary Insitute (SVA), Sweden (Coordinator)

**From Ulrike:**
Prof. William Cookson or Prof. Miriam Moffatt

**EMBARK WEBINAR 2022**
=========================================
# Dates (and speakers accepted 2022)

- March 16: **Windi Muziasari** ([e-mail])
- Junior speaker: **Anna Abramova** ([e-mail])
- Moderator: Johan
- April 13: **Ramanam Laxminarayan** ([e-mail])
- Junior speaker: **Zhao Cheng** ([e-mail])
- Moderator: Johan
- May 18: **Nichole Broderick** ([e-mail])
- Junior speaker: **Filipa Grosso** ([e-mail])
- Moderator: Victor
- June 15: **Marisa Haenni** ([e-mail])
- Junior speaker: **Reshma Silvester** ([e-mail])
- Moderator: Victor
- September 14: **Jon Hobman** ([e-mail])
- Junior speaker: **Kenyum Bagra**
- Moderator: Victor
- October 5: **Stineke van Houte** ([e-mail])
- Junior speaker: **Ruben V. Uribe**
- Moderator: Ulrike
- November 9: **Iruka Okeke** ([e-mail])
- Junior speaker: **Miranda J. Wallace**
- Moderator: Victor
- December 15: **Joakim Larsson** ([e-mail])
- Junior speaker: **Antti Karkman**
- Moderator: Svetlana

# Specific details for the talks

### March 16
**Dr. Windi Muziasari**
*Resistomap CEO*

**Global database of ARGs in the environment**

**Bio:** Dr. Windi Muziasari has gained years of experience and the know-how to monitor antibiotic resistance from environmental samples such as wastewater, rivers, lakes, soils and manure using a high-throughput gene profiling during her PhD and PostDoc at the University of Helsinki. She wanted other researchers at universities, research institutions and hospitals to gain easy access to this technology and that was why she moved from academia to entrepreneurship by founding Resistomap in 2018. Resistomap is the first company in the world to commercialize antibiotic resistance monitoring service in the environment. Headquartered in Helsinki, Resistomap's mission is to mitigate the spread of antibiotic resistance by providing robust tools for monitoring. Resistomap combines the molecular genetics method and data science to provide a service for antibiotic resistance monitoring comprehensively and fast. Since fully operating in January 2019, Resistomap has served over 140 projects from 28 countries.


### April 13
**Dr. Ramanam Laxminarayan**
*Director of the Center for Disease Dynamics, Economics & Policy (CDDEP)*

**State of the World’s Antibiotics 2022**

**Bio:** Laxminarayan is founder and director of the Center for Disease Dynamics, Economics & Policy (CDDEP) in Washington, D.C., a senior research scholar at Princeton University and affiliate professor at the University of Washington. Since 1995, Laxminarayan has worked to improve the understanding of antibiotic resistance as a problem of managing a shared global resource. His work encompasses extensive peer-reviewed research, public outreach, and direct engagement across Asia and Africa. Through his prolific research, and active public outreach (including a widely viewed TED talk) he has played a central role in bringing the issue of drug resistance to the attention of leaders and policymakers worldwide and to the United Nations General Assembly in September 2016. Laxminarayan served on the President Obama's Council of Advisors on Science and Technology’s antimicrobial resistance working group and is a voting member of the U.S. Presidential Advisory Council on Combating Antimicrobial Resistance. He is series editor of the Disease Control Priorities for Developing Countries, 3rd edition. In 2019, he received the the Birla Institute of Technology and Science's Distinguished Alumnus Award.

# Suggestions for EMBARK webinar speakers

## From Svetlana:

- Iruka Okeke *(pretty much accepted)*
https://twitter.com/iruka_okeke
- Augustina Sylverken *(invited)*
https://www.aasciences.africa/affiliate/sylverken-augustina-angelina-nee-annan
[e-mail]

- Yunsong Yu
[e-mail]
https://person.zju.edu.cn/en/yuyunsong
https://www.sciencedirect.com/science/article/abs/pii/S1198743X21006406

- Zhiyong Zong
[e-mail]
https://orcid.org/0000-0002-7675-260X
https://journals.asm.org/doi/10.1128/msystems.00831-21

*Chinese colleagues are collaborators in the project https://twitter.com/DETECTIVE_AMR with Alan Walker and Willem van Schaik!

NOTE: @CHARM_UCSD 2022 Virtual Seminar Series: https://twitter.com/victornizet/status/1488991134026137600

- [Abiola O. Olaitan](https://scholar.google.fr/citations?user=IMCwfV4AAAAJ&hl=en) from https://ibt.tamu.edu/centers/infectious-and-inflammatory-diseases/hurdle-lab/index.html
https://twitter.com/palmer_lab/status/1575185012940382208

- Aleksandra Petrovic Fabijan
[L-Form Switching in Escherichia coli as a Common β-Lactam Resistance Mechanism](https://journals.asm.org/doi/10.1128/spectrum.02419-22)
https://twitter.com/PetrovicFabijan

- Alison Mather [[e-mail]]
Latest paper: Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics
https://twitter.com/ae_mather/status/1583480782114680834

- Huiluo Cao, Hong Kong University
Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – Antimicrobial Chemotherapy
https://journals.asm.org/doi/10.1128/msystems.00775-22

## From Victor:
The first three are more related to the study of ARG and AMR in domestic animals and food. The last option is working mainly with the transmission of Salmonella in the food chain, but she has some works on AMR and works in a non-European institution, so perhaps that would expand a bit the scope from our webinars.

- Marisa Haenni *(invited)*
Anses Laboratoire de Lyon, Lyon, France
- Jon Hobman *(accepted)*
University of Nottingham, Nottingham, United Kingdom
- Herbert Tomaso
Friedrich-Loeffler-Institute Federal Research Institute for Animal Health, Greifswald, Germany
- Andrea Isabel Moreno Switt *(invited)*
Assistant Professor, Pontificia Universidad Católica de Chile
- Luck McNally
University of Edinburgh

**Junior options**
- Laura de Nies, Université du Luxembourg:
- PhD on Microbiome reservoirs of antimicrobial resistance
[ Mobilome-driven segregation of the resistome in biological wastewater treatment](https://www.biorxiv.org/content/10.1101/2021.11.15.468621v1)
- Melanie Schneider https://orcid.org/0000-0002-7085-6731

- Bernardo Ribeiro da Cunha https://orcid.org/0000-0002-0303-9416

## From Johan:

- Joakim Larsson *(accepted)*
University of Gothenburg, Sweden
- Yngvild Wastesson
NMBU, Norway (CORNELIA project)
- Barth Smets
University of Copenhagen, Denmark (DARWIN project)
- Windi Muziasari
Resistomap, Finland
- Volga Iñiguez
UMSA, Bolivia
- Thomas van Boeckel
ETH Zurich, Switzerland
- Ramanam Laxminarayan *(accepted)*
USA/India
- Nicole Broderick *(accepted)*
John Hopkins Medical School, USA (Tiny Earth)
- Jose Luis Martinez
Spain
- John Hays
Erasmus MC, the Netherlands (Seq4AMR Consoritum)

## From Uli:
- Stineke van Houte *(accepted)*
University of Exeter
Use of CRISPR-Cas systems to alter microbial communities, with a particular focus on removing antimicrobial resistance genes
https://biosciences.exeter.ac.uk/staff/profile/index.php?web_id=Christina_Van_Houte
- Helmut Bürgmann
Eawag
Dissemination and evolution of antimicrobial resistance in the aquatic environment.
https://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/helmut-buergmann/show/
- Jamie Hall
University of Liverpool
Evolutionary ecology of plasmid-mediated horizontal gene transfer
https://www.liverpool.ac.uk/infection-veterinary-and-ecological-sciences/staff/james-hall/
- Tong Zhang
Hong Kong University