Category: Workshops

Biocides and antibiotic resistance workshop

The newly formed BIOCIDE program, seeking to determine how antibacterial biocides contribute to the development of biocide resistance and spread of antibiotic resistant bacteria, is organizing a workshop on risk assessment of biocide and antibiotic resistance on the 9th of March this year. I will be giving a talk on the BacMet database and how that will be integrated in risk assessment and the research program. If you have an interest in the risk associated with biocides, or antibiotic resistance development, I strongly suggest that you take part in this exciting workshop, particularly if you are working for a regulatory authority.

The program targets biocide resistance and cross-resistance to antibiotics, guidance development for assessment of biocide resistance, the BacMet biocide resistance database, and the assessment of environmental exposure to biocides and risks for co-selection. The workshop will include speakers such as Joakim Larsson, Nabila Haddache, Marlene Ågerstrand and Frank Schreiber.

More information can be found here:


And like that, the world had changed

I guess it hasn’t passed anyone by that we are under a global lockdown (although to very different degrees – Sweden, where we’re based, has a pretty relaxed attitude to quarantining people (1), so it could be worse for us, I guess). In any case, the novel coronavirus has forced the lab to largely work from home and has upended essentially all my plans for this spring, expect for writing grant applications (which I have done a lot).

First of all, I want to thank my fellow lab members for holding out strongly in these trying times. They have consistently shown that they are the best co-workers I could ask for, and have kept calm even when anxiety hits. Thanks a lot for that. I also would like to thank the university for providing rather clear guidance on how to handle different issues that come up in these time of crisis.

With that said, I am also sad to say that there will not be a Microbiome & Probiotics Collaboration Forum in Rotterdam on May 18-20. Instead that meeting has been postponed to early December. Similarly, I will not be in Helsinki next week to talk about EMBARK. That workshop will instead, hopefully, take place on August 28. And the same story goes for the NordicMappingAMR organised by the Swedish Medical Products Agency, which will take place at a later date (I am not sure exactly when this is planned yet).

These are trying times for all of us. I hope that you stay healthy and take care of your loved ones – particularly the elderly, but not unnecessarily visiting them. My grandparents (aged 93 and 95) have started FaceTiming us, so I guess some good things come out of this mess as well. We will come out of this crisis stronger, eventually.


  1. There are many things I could say about the Swedish strategy regarding covid-19, but this is not really the forum. In very brief, though, I have quite some faith in that the Swedish Public Health Agency is doing a decent job. Mistakes have been made (particularly early in the pandemic) and I am slightly anxious whether the Swedish strategy will play out as well as in other countries in Northern Europe, but right now data suggest that we are doing reasonable fine. I might return to this issue in another post if time permits.

Swedish Bioinformatics Workshop 2019

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!

Talk on emission limits in Stockholm

In two weeks time, on the 15th of June, I will participate in a seminar organised by Landstingens nätverk för läkemedel och miljö (the Swedish county council network for pharmaceuticals and environment; the seminar will be held in Swedish) in Stockholm. I will give a talk on our proposed emission limits for antibiotics published last year (the paper is available here), but there will also be talks on wastewater treatment, sustainable pharmaceutical usage and environmental standards for pharmaceuticals. The full program can be found here, and you may register here until June 9. The seminar is free of charge.

And if you are interested in this, I can also recommend the webinar given by Healthcare Without Harm next week (on June 8), which will deal with sustainable procurement as a means to deal with pharmaceutical pollution in the environment. I will at least tune in to hear how the discussion goes here.

Report on JRC AMR workshop

In March, I attended a workshop on the role of NGS technologies in the coordinated action plan against antimicrobial resistance, organised by JRC in Italy. I was, together with 14 other experts, invited to discuss where and how sequencing can be used to investigate and manage antibiotic resistance. The report from the workshop has just recently been published, and is available here. There will be follow-up activities on this workshop, which I also hope that I will be able to participate in, since this is an important and very interesting pet topic of mine.


  • Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099 [Link]
  • Webinar on Antimicrobial Resistance and the Environment

    I will give a short talk on our findings related to antibiotic resistance associated with pharmaceutical production facilities in India at a one-hour webinar arranged by Healthcare Without Harm, taking place on Thursday, November 3rd, 10.00 CET. The webinar will discuss “hot-spot” environments in which antimicrobial resistance can emerge, such as areas in which there are poor pharmaceutical manufacturing practices, where expired or unused drugs are disposed of in an inappropriate way (i.e. by flushing them down the toilet or sink, or disposing them in household rubbish), and areas in which pharmaceuticals are used for aquaculture or agriculture. This is an important aspect of the resistance problem, but to date most of the actions taken to tackle the spread of AMR don’t take into account this aspect of antimicrobials released into the environment. The webinar is co-organised by HCWH Europe and HCWH Asia, and aims to raise awareness about the issue of AMR and its environmental impact. It features, apart from myself, Lucas Wiarda (Global Marketing Director & Head of Sustainable Antibiotics Program at DSM Sinochem Pharmaceuticals) and Sister Mercilyn Jabel (Pharmacist at Saint Paul Hospital Cavite, Philippines).

    Sign up here to learn about:

    • Antibiotic pollution and waste
    • Recent findings from India regarding antibiotic discharges in rivers from manufacturers and new mechanisms by which resistance spreads in the environment
    • Sustainable antibiotics – how to support the proper and effective use of antibiotics and their responsible production
    • How the pharmaceutical industry is addressing the environmental pollution that leads to AMR
    • The best practices in managing infectious waste at hospital level


    Today the 15th Swedish Bioinformatics Workshop starts in Linköping. For the first time in many many years, I will not be there, which feels super-strange. (I even took part in organizing the workshop two years ago, in Gothenburg.) I would have thoroughly enjoyed the schedule (the workshops look amazing), and hope that everyone will have a very good time there without me. I do miss you! Please make sure I get another opportunity next year!

    Annual GOTBIN Meeting on December 6

    I am part of the organizing committee for the newly invented annual meeting for GOTBIN – the Gothenburg Bioinformatics Network. We will arrange a meeting on December 6 to get the networking activities for 2017 kickstarted, and every bioinformatician in Gothenburg is invited!

    GOTBIN was launched to bridge and bring together all researchers in Gothenburg who fully or partially dealt with bioinformatics in their research. Through the network it should be possible to quickly find other local researchers tackling the same research problems as you are; to find appropriate resources to run your analyses; and to discuss research or infrastructure problems as they arise. To keep the network alive and kicking, it is crucial to keep relations active. Furthermore, it is also crucial to interact with key persons in the GOTBIN network to keep the lists of active researchers, resources and discussion forums up to date.

    To facilitate future communication, we invite everyone who works with bioinformatics in Gothenburg to participate in a get-together workshop. The purpose of this workshop is to find out who is working with what and where, and to better get to know each other. This is a great opportunity to meet your next collaboration partner, post-doc or supervisor! The event will take place in Birgit Thilander at Medicinareberget (just next to the large lecture hall Arvid Carlsson) on December 6th, from 9.00 to 12.00. Fika will be provided and we will arrange ice-breaker activities suitable for the number of participants, so please register at: by the 16th of November.

    We hope to find everyone with a research interest in bioinformatics there and that this will be the launch of the next era of GOTBIN in 2017! See you there!

    Database quality paper in special issue

    I just want to highlight that the paper on strategies to improve database accuracy and usability we recently published in Proteomics (1) has been included in their most recent issue, which is a special issue focusing on Data Quality Issues in Proteomics. I highly recommend reading our paper (of course) and many of the other in the special issue. Happy reading!

    On another note, I will be giving a talk next Wednesday (October 5th) on a seminar day on next generation sequencing in clinical microbiology, titled “Antibiotic resistance in the clinic and the environment – There and back again“. You are very welcome to the lecture hall at floor 3 in our building at Guldhedsgatan 10A here in Gothenburg if you are interested! (Bear in mind though that it all starts at 8.15 in the morning.)

    Finally, it seems that I am going to the Next Generation Sequencing Congress in London this year, which will be very fun! Hope to see some of you dealing with sequencing there!


    1. Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sánchez J, Sanli K, Thorell K: Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics, 16, 18, 2454–2460 (2016). doi: 10.1002/pmic.201600034 [Paper link]