Category: Conferences

I have written an editorial piece for the Swedish Pathogens Portal in which I reflect a bit on the upcoming EU legislation requiring monitoring of AMR in major wastewater treatment plants (1). I also veer a bit into where environmental monitoring outside of sewage may play a role, using our review paper resulting from EMBARK as the starting point (2).

This is timed to coincide with the registration deadlines for two upcoming workshops on AMR surveillance in the environment; the first being the DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Disease on 7th-8th October in Uppsala, which I have been part of organising. The second is a workshop organised by CARe in Gothenburg on 28th October on the theme of sewage surveillance of antibiotic resistance, focusing on the new EU requirements.

My hope is that you will be a bit provoked by this and come to one of these workshops to discuss AMR surveillance and where to go next!

1. Bengtsson-Palme J: Surveillance of antimicrobial resistance – flying blind or flying behind? The Swedish Pathogens Portal, Editorial (2024). doi: 10.17044/scilifelab.27045433 [Link]
2. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 178, 108089 (2023). doi: 10.1016/j.envint.2023.108089 [Paper link]

Together with Anna Székely, I have been working on the organization of a DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases on October 7 – 8, in Uppsala.

The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches. We now invite submission of abstracts for short talks.

Deadline for abstract submission: 18 September 
Deadline to register to attend: 25 September –> REGISTER HERE! <– This includes abstract submission.

Link to more information and the PROGRAM

I hope to see all of you working with AMR in the environment in Uppsala in October!

Ákos Kovács had the brilliant idea of putting up a temporary resource for things you bring up in a talk that you can point people to. I did not do this before my talk at ISME today, but I thought the idea was so good, so here’s a summary and collection of my ISME short-talk on the EMBARK outcomes today:

• More information on EMBARK and its successor SEARCHER can be found on the project website, here: http://antimicrobialresistance.eu Importantly, this is a team effort over four years and I only touched on a few selected things
• Within the project we have looked at typical background levels of antibiotic resistance in the environment. We have already published some of these results (for qPCR abundances) in Abramova et al. 2023
• The average resistance gene in the average environment is present in ~1 in 1000 bacteria, but the variation between different genes is huge
• Depending on monitoring goal, different target genes are relevant to use. See this table adapted from Abramova et al. 2023:

• We have also tried to make different monitoring methods for environmental AMR comparable. Those mentioned in the talk were selective culturing for resistant bacteria, qPCR and shotgun metagenomics
• This data is not yet published, but overall we see relatively good correlation between qPCR and metagenomics. This is not true for all genes, though, and unfortunately neither qPCR nor metagenomics is always better than the other
• Culturing data is not very good at predicting specific antibiotic resistance gene abundances as the class level
• Finally, we have developed methods for discovering new types of ARGs, as seen in the ResFinderFG database: Gschwind et al. 2023
• We have also used these new methods to look at differences between established ARGs and latent ARGs in a variety of environments: Inda-Díaz et al. 2023
• Our ultimate goal in EMBARK would be to develop a modular framework for environmental monitoring of antibiotic resistance. You can read more about our thinking and goals in the review paper we published last year: Bengtsson-Palme et al. 2023

Time to do a rundown of conferences and meetings I will attend this fall. Double-check with your calendars and please reach out if you’re also going, so we can meet up!

September 21-24: Nordic Society of Clinical Microbiology and Infectious Diseases (NSCMID), in Örebro, Sweden. I will give a talk about the EMBARK work in the Saturday session on Metagenomics in infection, inflammatory disease and the environment

October 5-6: Conference on ‘Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain’ organised by The Netherlands Food and Consumer Product Safety Authority (NVWA) in Amsterdam, the Netherlands. I will chair a session on October 6 on Next generation sequencing for bioinformatic based surveillance.

October 18-22: 32º Congresso Brasileiro de Microbiologia, in Foz do Iguaçu, Brazil. I will give a talk in the Saturday session (the 21st) on the use of model systems all the way to global surveillance systems to prevent future pandemics.

November 15-16: DDLS Annual Meeting, in Stockholm Sweden. I am in the organising committee for this event with the theme “The emerging role of AI in data-driven life science”.

November 17: DDLS Cell and Molecular Biology Minisymposium.

November 29: GOTBIN Annual Workshop, in Gothenburg Sweden.

This will be a fun (but intense!) fall!

On the 5th and 6th of October this year, I will be taking part in a relatively small, but very interesting conference on veterinary and environmental AMR, held in Amsterdam. The theme of the event will be “Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain”.

The aim of the conference is to discuss innovative additional measures to prevent development of resistance in animals. In addition, the participants will explore possibilities to prevent transfer to human health care after selection has taken place. The conference program will consist of both lectures and break-out sessions and is intended for researchers as well as for policy makers involved in the battle against antimicrobial resistance. The results of the break-out sessions are to be published in an open access journal, and I will be charing one of these break-out sessions. Please see the conference web site for the entire program: https://www.nvwa.nl/amrconference

There is an upper cap of 120 participants for the event, so if you’re interested make sure to register soon! The conference will be held on October 5 and 6 2023 in the Park Inn by Radisson in Amsterdam, The Netherlands. The hotel is easy to reach by a 12 minutes train ride from Schiphol airport and a 5 minutes train ride from the city center. 

I look forward to seeing you in Amsterdam!

I will be giving talks on data driven life science – specifically on antibiotic resistance and pathogenicity – on two different events organised within the Data Driven Life Science program (DDLS) in the next month. First up is on the DDLS Annual Conference, coming up already next week (15-16 November). Here, I will give a talk on the evolution of pathogenicity, outlining some of our ongoing work towards finding novel virulence factors. There will also be talk from the other DDLS fellows, as well as Samuli Ripatti and Cecilia Clementi.

On-site registration closes on November 9 so make sure to grab one of the last spots at this exciting event! Register here – online attendance is also possible for those who don’t want to travel to Stockholm.

Then in December, I will be talking at the Data-driven Epidemiology and biology of infections Research Area Symposium in Gothenburg on how to predict the disease threats of the future. This symposium takes place in Gothenburg on December 7 to 8, but again online participation is also possible. Aside from me, Nicholas Croucher will talk about genomic surveillance data and bacterial epidemiology, Bill Hanage will talk about decisions in an imperfect world and Tove Fall will talk about dynamic disease surveillance. There will also be talks about the new DDLS fellows in epidemiology and infection biology, which is what I am perhaps most excited about: Thomas van Boeckel, Luisa Hugerth and Laura Carroll! It seems like registration has not yet opened for this event, but keep monitoring this site.

I look forward to see you at these events!

This week, in a stroke of luck coinciding with my conference presentation on the same topic, my review paper on microbial model communities came out in Computational and Structural Biotechnology Journal. The paper (1) provides an overview of the existing microbial model communities that have been developed for different purposes and makes some recommendations on when to use what kind of community. I also make a deep-dive into community intrinsic-properties and how to capture and understand how microbes growing together interact in a way that is not predictable from how they grow in isolation.

The main take-home messages of the paper are that 1) there already exists a quite diverse range of microbial model communities – we probably don’t need a wealth of additional model systems, 2) there need to be better standardization and description of the exact protocols used – this is more important in multi-species communities than when species are grown in isolation, and 3) the researchers working with microbial model communities need to settle on a ‘gold standard’ set of model communities, as well as common definitions, terms and frameworks, or the complexity of the universe of model systems itself may throw a wrench into the research made using these model systems.

The paper was inspired by the work I did in Jo Handelsman‘s lab on the THOR model community (2), which I then have brought with me to the University of Gothenburg. In the lab, we are also setting up other model systems for microbial interactions, and in this process I thought it would be useful to make an overview of what is already out there. And that overview then became this review paper.

The paper is fully open-access, so there is really not much need to go into the details here. Go and read the entire thing instead (or just get baffled by Table 1, listing the communities that are already out there!)

References

1. Bengtsson-Palme J: Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal, in press (2020). doi: 10.1016/j.csbj.2020.11.043
2. Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J: Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio, 10, 2, e02846-18 (2019). doi: 10.1128/mBio.02846-18

As I have been indicating before, I will be presenting at the Microbiome & Probiotics Collaboration Forum in Rotterdam on May 18-20. In relation to this, I was asked to write a shorter blog post on (or, if you will, some type of extended abstract) what I will talk about, which is how simple model systems for microbial communities can be used to understand complex systems with loads of interactions, similar to how E. coli and yeast have enabled a much more wide-reaching understanding of molecular biology than just about those two single-celled organisms themselves. The entire post can be read here, and I hope that I will see you in Rotterdam in May!

Here’s some updates on my Spring schedule.

On March 19, I will be presenting the EMBARK program and what we aim to achieve at a conference organised by the Swedish Medical Products Agency called NordicMappingAMR. The event will feature an overview of existing monitoring of antibiotics and antibiotic resistant bacteria in the environment. The conference aims to present the results from this survey, to listen to experts in the field and to discuss possible progress. It takes place in Uppsala. For any further questions, contact Kia Salin at NordicMappingAMR@lakemedelsverket.se

Then on May 18 to 20 I will participate in the 7th Microbiome & Probiotics R&D and Business Collaboration Forum in Rotterdam. This industry/academia cross-over event focuses on cutting-edge microbiome and probiotics research, and challenges and opportunities in moving research towards commercialisation. I will talk on the work we do on deciphering genetic mechanisms behind microbial interactions in microbiomes on May 20.

And finally, I also want to bring the attention to that my collaborator Erik Kristiansson has an open PhD position in his lab. The position is funded by the Environmental Dimensions of Antibiotic Resistance (EDAR) research project, aiming to describe the environmental role in the development and promotion of antibiotic resistance. The focus of the PhD position will be on analysis of large-scale data, with special emphasis on the identification of new forms of resistance genes. The project also includes phylogenetic analysis and development of methods for assessment of gene evolution. More info can be found here.

The final schedule is out for the Swedish Bioinformatics Workshop (SBW) 2019! I will be there (after all, it is in Gothenburg and I am in the organising committee…) and will give a workshop on sequence annotation errors on Monday afternoon. And then on Tuesday afternoon, I will participate in a panel discussion on careers in computational biology, organised by RSG-Sweden. I hope I will see you there!