Tag: Antibiotic resistance

Pandemic Preparedness Portal

I am happy to announce that I am joining the editorial committee of the Swedish Pandemic Preparedness Data Portal (formerly the Swedish COVID-19 portal). I will join five other researchers associated with SciLifeLab and will work together with the portal team to maximise the utility of the Portal for researchers, expand its content beyond SARS-CoV-2, and increase engagement with the research community. My main responsibility areas will be antibiotic resistance and emerging pathogens.

Since 2022 the portal is part of the SciLifeLab Pandemic Laboratory Preparedness (PLP) Program. It is operated by the SciLifeLab Data Centre. Over time, the popularity of the Portal has increased within the research community, the general public, and those involved in healthcare, industry, and policy making. I very much look forward to work with Luisa Hugerth (Uppsala University), Laura Carroll (Umeå University), Benjamin Murrell (Karolinska Institute), Mahmoud Naguib (Uppsala University) and Johan Ankarklev (Stockholm University) on the future of the portal!

Published report: UNEP One Health AMR response

UNEP last week published their report on one health responses to antimicrobial resistance (1), which I have taken part in writing (well, I think I ultimately only contributed a few sentences here and there, but apparently that counts to be listed among the report’s contributors). The report, named “Bracing for Superbugs: Strengthening environmental action in the One Health response to antimicrobial resistance” showcases the evidence for that the environment plays a key role in the development, transmission and spread of AMR.

The report tries to unpack the different aspects of environmental AMR, and offers a fairly comprehensive picture of where the science stands on the subject. We also conclude that a systems effort – “One Health” – recognizing that the health of people, animals, plants and the environment are closely connected, is needed to tackle AMR.

This report analyzes the three economic sectors and their value chains that are key drivers of AMR development and spread in the environment: pharmaceuticals and other chemicals, agriculture including the food chain, and healthcare, together with pollutants from poor sanitation, sewage and waste effluent in municipal systems.

I am very happy to have been part of this report writing team and I hope that this will spur future action on AMR from a one-health perspective. You can read the entire report here.

Reference

  1. United Nations Environment Programme (2023). Bracing for Superbugs: Strengthening environmental action in the One Health response to antimicrobial resistance. Geneva

Welcome Vi and Marcus

I am very happy to share with you that our two doctoral students funded by the Wallenberg DDLS initiative have now started. One of them – Marcus Wenne – is already a well-known figure in the lab, as he has been with us as a master student and then as a bioinformatician for more than a year. The other student – Vi Varga – is a completely new face in the lab and just started yesterday.

Marcus will work in a project on global environmental AMR. He will also continue on his work on large-scale metagenomics to understand community dynamics and antibiotic resistance selection in microbial communities subjected to antibiotics selection. Marcus will work very closely to EMBARK and continue the important work we have done in that project over the next four years.

Vi will study responses of microbial communities to change, with a particular focus on comparative genomics and transcriptional approaches. We will link this to both community stability, pathogenesis and resistance to antibiotics, so this project involves a little bit of everything in terms of the lab’s research interests. Vi’s background is in comparative genomics and pathogenesis, so this seems to be the perfect mix to be able to carry out this project successfully!

Very welcome to the lab Marcus and Vi! We look forward to work with you for the next four years or so!

Einhorn SIGHT Award

It’s been a busy couple of days at the DDLS Annual Meeting, so I did not have the time to post about this exciting news yesterday, but it is very exciting nonetheless.

I have been selected by the board of the Royal Swedish Academy of Sciences as the 2022 recipient of the Einhorn SIGHT award. The award recognizes outstanding global health research work by young researchers in the context of low- and middle-income countries, and specifically I have been selected thanks to my “outstanding research and development of tools to limit the global challenge of infectious diseases and antibiotic resistance.”

In a global health context, what is particularly important in the coming years is improved access to clean water and sewage systems. In addition, we also need to develop data-driven systems that can be used to implement easy-to-handle, inexpensive early warning systems and risk models for antibiotic-resistant bacteria, which we hope will be the outcome of the EMBARK program.

Clearly, a large part of this is the result of the work the entire EMBARK team has put together in the past couple of years. Another big part has been the work I have done together with Joakim Larsson in the area of antibiotic resistance in the environment. I am deeply grateful both to Joakim and my EMBARK collaborators for their contributions towards this award. Science is a teamwork, and it is a bit of a pity that we celebrate individuals to the extent we do (even though the recognition of my contribution of course is nice for me personally). Thanks to everyone who have been involved over the years!

There will be an award ceremony at the Royal Academy of Sciences on November 22, as part of a very nice event on Global Health, with the theme ‘Food Safety in conflict’. You can read a short interview I did in relation to the award here.

In other notes, I was also selected as one of Clarivate as one of this year’s Highly Cited Researchers (for the third year in a row!) This is of course also exciting news, although the most important aspect of that is that it shows that the research we do is useful to others!

DDLS Talks

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!

September 2022 Pod: Environmental Antibiotic Resistance

Finally the lab podcast is back! In this episode Microbiology Lab Pod, the team (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Mirjam Dannborg and Agata Marchi) discusses the environmental antibiotic resistance in anticipation of the EDAR conference coming up later this week!

The specific papers discussed in the pod are as follows:

  • Marcoleta, Andrés E., Patricio Arros, Macarena A. Varas, José Costa, Johanna Rojas-Salgado, Camilo Berríos-Pastén, Sofía Tapia-Fuentes, et al. “The Highly Diverse Antarctic Peninsula Soil Microbiota as a Source of Novel Resistance Genes.” Science of The Total Environment 810 (March 2022): 152003. https://doi.org/10.1016/j.scitotenv.2021.152003
  • Yi, Xinzhu, Jie-Liang Liang, Jian-Qiang Su, Pu Jia, Jing-li Lu, Jin Zheng, Zhang Wang, et al. “Globally Distributed Mining-Impacted Environments Are Underexplored Hotspots of Multidrug Resistance Genes.” The ISME Journal 16, no. 9 (September 2022): 2099–2113. https://doi.org/10.1038/s41396-022-01258-z
  • Johnning, Anna, Erik Kristiansson, Jerker Fick, Birgitta Weijdegård, and DG Joakim Larsson. “Resistance Mutations in GyrA and ParC Are Common in Escherichia Communities of Both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments.” Frontiers in Microbiology 6 (2015): 1355. https://doi.org/10.3389/fmicb.2015.01355
  • Flach, Carl-Fredrik, Chandan Pal, Carl Johan Svensson, Erik Kristiansson, Marcus Östman, Johan Bengtsson-Palme, Mats Tysklind, and D. G. Joakim Larsson. “Does Antifouling Paint Select for Antibiotic Resistance?” The Science of the Total Environment 590–591 (July 15, 2017): 461–68. https://doi.org/10.1016/j.scitotenv.2017.01.213

The podcast was recorded on September 12, 2022. If you want to reach out to us with comments, suggestions, or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.

Thanks for the applications

Our open doctoral student and postdoc positions closed over the weekend, and in total we had 110 applications, although some persons applied to more than one of the positions, bringing the total number of applicants down a bit. Still, this will be a lot of work for me. I will prioritize the postdoc position, as this had the fewest applications. So if you applied to one of the two PhD student positions, please give it some time.

A quick skimming of the applications shows that we have had extraordinary high quality of applications overall, although some of the applicants will be a bit too wet-lab oriented for these specific positions.

Thanks a lot for your interest in the lab’s work! I appreciate all of your efforts!

We’re hiring 2 PhD students and a postdoc

As I wrote a few days ago, I have now started my new position at Chalmers SysBio. This position is funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), which also funds PhD and postdoc positions. We are now announcing two doctoral student projects and one postdoc project within the DDLS program in my lab.

Common to all projects is that they will the use of large-scale data-driven approaches (including machine learning and (meta)genomic sequence analysis), high-throughput molecular methods and established theories developed for macro-organism ecology to understand biological phenomena. We are for all three positions looking for people with a background in bioinformatics, computational biology or programming. In all three cases, there will be at least some degree of analysis and interpretation of large-scale data from ongoing and future experiments and studies performed by the group and our collaborators. The positions are all part of the SciLifeLab national research school on data-driven life science, which the students and postdoc will be expected to actively participate in.

The postdoc and one of the doctoral students are expected to be involved in a project aiming to uncover interactions between the bacteria in microbiomes that are important for community stability and resilience to being colonized by pathogens. This project also seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. The project tasks may include things like predicting genes involved in pathogenicity and other interactions from sequencing data, and performing large-scale screening for such genes in microbiomes.

The second doctoral student is expected to work in a project dealing with understanding and limiting the spread of antibiotic resistance through the environment, identifying genes involved in antibiotic resistance, defining the conditions that select for antibiotic resistance in different settings, and developing approaches for monitoring for antibiotic resistance in the environment. Specifically, the tasks involved in this project may be things like identifying risk environments for AMR, define potential novel antibiotic resistance genes, and building a platform for AMR monitoring data.

For all these three positions, there is some room for adapting the specific tasks of the projects to the background and requests of the recruited persons!

We are very excited to see your applications and to jointly build the next generation of data driven life scientist! Read more about the positions here.

Open postdoc position

Together with Joakim Larsson‘s lab, we now have an open two-year postdoc position in bioinformatics on antibiotic resistance and biocide resistance. The development of antibiotic resistance has been driven by use of antibiotics, but antibacterial biocides also have the potential to select for antibiotic resistance. However, knowledge of which genes that contribute to biocide resistance and could be associated with antibiotic resistance is sparse. To some extent, such genes are documented in the BacMet database which we have developed, but this collection of resistance genes is only scratching the surface of all biocide resistance that exists among bacteria in the environment.

We are now looking for a postdoctoral fellow to continue the important work on bioinformatic analysis of biocide and antibiotic resistance to answer the question whether increasing biocide resistance would be a threat to human health. The postdoc will be working with the development of the BacMet database to make it more targeted towards biocidal substances and products in addition to resistance genes. The tasks include bioinformatic sequence analysis, literature studies and database and web programming. The work will also include investigations of the prevalence of the identified resistance genes in genomes and metagenomes.

The recruited person will work closely with both my group and the group of Prof. Joakim Larsson, and will participate in the JPIAMR-funded BIOCIDE project. You can apply to the postdoc position at the University of Gothenburg application portal: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=25122

The deadline is May 4, 2022. Come work with us on this exciting topic in the intersect between two great research environments (if I may say it myself!) We look forward to your application!