Category: Lab

I’ve been terribly bad at keeping updates on what we have published in the last year or so – there have just been a bit too much other things to do. So I thought it was time to take a look at what we have published in the last year before some really cool stuff hits the press this summer and fall (hopefully more on that soon!!)

Let’s start with some EMBARK/SEARCHER output. Several lab members (Anna, Marcus and I) have been involved in a paper using functional metagenomics to find novel cefiderocol resistance genes (1). We found four resistance genes, including three ꞵ-lactamases (VEB-3, an OXA-372 homolog, and a YbxI homolog) and a partial penicillin-binding protein homolog, none of which had been previously reported as a cefiderocol resistance gene. The blaVEB-3 gene was associated with a mobile genetic element. We could find three of them using shotgun metagenomics, showing that the blaVEB-3 gene was widespread across France, Sweden, Germany and Pakistan, hinting at efficient dissemination of this gene.

I have also been involved in a collaboration paper with Thomas Berendonk and Uli Klümper‘s labs, where we investigate if fish can be sentinels of environmental antibiotic resistance, and it turns out that they are… not great for that (2).

On the topic of antibiotic resistance gene (ARG) dissemination, Máté Vass (now at SLU) lead a study published in Communications Biology investigating how water stratification affects horizontal gene transfer, with a focus on ARGs (3). The main finding of this paper is that water stratification is a constraint on horizontal gene transfer, which may have implications on how we think about ARG spread through water environments.

While we are at the topic of large-scale quantifications of ARGs in big data sets, I was super-happy to be part of a collaboration with Katariina Pärnänen on how gender (and other factors) impact ARGs in the human microbiome (4). I kept telling Katariina that this would probably yield nothing – the microbiome data was too noisy, and the signal will get lost. Yet, she persisted, and indeed it turned out we are at the point where there is enough human microbiome data to get a signal even if there is a lot of noise. So hats off to Katariina, this was your “what did I say” moment with me!

Then we have a set of mechanistic AMR studies on ARG evolution. First, Lisa Teichmann published parts of her PhD thesis, first on the gradual evolution of fluoroquinolone resistance in E. coli (5) and how this is related to the SOS response in bacteria. She then followed up with a somewhat similar paper on amoxicillin evolution in E. coli (6). The general picture of these two papers on how E. coli adapts genetically to antibiotic stress is that resistance evolution is highly antibiotic-specific and that canonical stress-response or mutagenic pathways do not uniformly explain adaptive trajectories.

Somewhat connected, Nathália Abichabki recently published a paper where we propose screening cut-off values and tolerance disk tests (TDtests) for detection of tolerance/persistence to ceftazidime-avibactam in Klebsiella pneumoniae (7). This is also related to a bunch of papers on tolerance and low-level resistance to antibiotics that will be coming out of Nathália’s thesis, so there is more coming on this front soon!

Finally – on the AMR front – Anna Abramova led an effort together with Veronika Pettersen to investigate possibility for integration of AMR surveillance systems in the Nordic countries that recently got published in Public Health (8). Anna and Veronika did a huge amount of work on this paper, but this was largely the outcome of several meetings on the NoMoReAMR consortium, where we pinpointed missed opportunities for surveillance in the otherwise relatively homogenous Nordic countries. I hope to get to work more with this consortium in the future, as I think that we have had very fruitful discussions on both AMR research and monitoring and when and where it is useful.

And so two papers not related to AMR: We had a very nice collaboration with Daniel Bojar‘s group coming out late last year in Nature Communications, looking – from many different angles – at seal milk oligosaccharides and their potential uses. While the cool finding in this paper is that seal milk seems even more complex than human breast milk in terms of milk oligosaccharides (9), we did not contribute too much in that part. Instead, Mirjam Dannborg was studying the effects of these oligosaccharides on pathogen biofilms, work that will also be part of her PhD thesis when she defends this fall!

Finally, in a collaboration with colleagues in Brazil, we published a review article on the outlook for combining 3D organoid cultures and high-throughput analysis techniques to better understand host-pathogen interactions (10). This was the result of a cross-visit collaboration between Brazil and Sweden, where me and Mirjam visited the lab of Elaine de Martinis, and Elaine, Leonardo Andrade and Nathália Abichabki visited our lab back in 2023. It’s nice to see our discussions take paper form and I hope to be working more with this wonderful team in Brazil!

Papers mentioned:

1. Gschwind R, Bonnet M, Abramova A, Jarquín-Díaz VH, Wenne M, Löber U, Godron N, Kampouris ID, Tskhay F, Nahid F, Debroucker C, Bui-Hai M, El Aiba I, Klümper U, Berendonk TU, Forslund-Startceva SK, Zahra R, Bengtsson-Palme J, Ruppé E: Cefiderocol resistance genes identified in environmental samples using functional metagenomics. ISME Journal, 20, 1, wrag010 (2026). doi: 10.1093/ismejo/wrag010 [Paper link]
2. Tskhay F, Köbsch C, Elena AX, Bengtsson-Palme J, Berendonk TU, Klümper U: Fish are poor sentinels for surveillance of riverine antimicrobial resistance. One Health, 20, 101026 (2025). doi: 10.1016/j.onehlt.2025.101026 [Paper link]
3. Vass M, Abramova A, Bengtsson-Palme J: Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters. Communications Biology, 9, 435 (2026). doi: 10.1038/s42003-026-09857-8 [Paper link]
4. Salehi M, Laitinen V, Bhanushali S, Bengtsson-Palme J, Collignon P, Beggs JJ, Pärnänen K, Lahti L: Gender differences in global antimicrobial resistance. npj Biofilms and Microbiomes, 11, 79 (2025). doi: 10.1038/s41522-025-00715-9 [Paper link]
5. Teichmann L, Luitwieler SH, Bengtsson-Palme J, ter Kuile BH: Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response. BMC Microbiology, 27, 37 (2025). doi: 10.1186/s12866-025-03771-5 [Paper link]
6. Teichmann L, Wenne M, Luitweiler S, Dugar G, Bengtsson-Palme J, ter Kuile B: Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE. PLoS ONE, 20, 2, e0312223 (2025). doi: 10.1371/journal.pone.0312223 [Paper link]
7. Abichabki N, Bellissimo-Rodrigues F, Gaspar GG, Pocente RHC, Lima DAFS, Bollela VR, Braga GUL, De Martinis ECP, Ferreira JC, Darini ALC, Bengtsson-Palme J, Andrade LN: Proposal for screening cut-off values and use of Tolerance Disk Test (TDtest) for detection of tolerance/persistence to ceftazidime-avibactam in Klebsiella pneumoniae. Diagnostic Microbiology and Infectious Disease, 116, 3, 117515 (2026). doi: 10.1016/j.diagmicrobio.2026.117515 [Paper link]
8. Abramova A, Baral A, Osińska AD, Metsä-Simola N, Räisänen K, Ribeiro Duarte AS, Helgason KO, Halldórsdóttir AM, Pärnänen K, Skov Simonsen G, Sariola S, Lahti L, Bengtsson-Palme J, Wasteson Y, Munk P, Pettersen VK: Roadmap for integrated One Health AMR surveillance in Nordic countries. Public Health, 255, 106285 (2026). doi: 10.1016/j.puhe.2026.106285 [Paper link]
9. Jin C, Lundstrøm J, Cori CR, Guu S-Y, Bennett AR, Dannborg M, Bengtsson-Palme J, Hevey R, Khoo K-H, Bojar D: Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation. Nature Communications, 16, 10067 (2025). doi: 10.1038/s41467-025-66075-2 [Paper link]
10. de Martinis ECP, Alves VF, Pereira MG, Andrade LN, Abichabki N, Abramova A, Dannborg M, Bengtsson-Palme J: Applying 3D cultures and high-throughput technologies to study host-pathogen interactions. Frontiers in Immunology, 16 (2025). doi: 10.3389/fimmu.2025.1488699[Paper link]

I am happy to share the news that my first doctoral student – Emil Burman – successfully defended his thesis yesterday, and can now introduce himself as Dr. Burman.

And in what a way he defended! During the three hour defense, he was asked all the hard questions from his opponent – Akos Kovács – who did an amazing job bringing out Emil’s vast and diverse knowledge of the field. In fact, the committee noted afterwards that it took more than one and a half hours of questioning before Emil had to admit “I don’t know the answer to that”.

Emil’s thesis, titled “Genetic Contributions to Invasion and Biofilm Disruption in a Microbial Model Community“, used the microbial model community THOR (1) to investigate community responses to environmental stress and microbial invasion. The thesis (2) consists of five papers, the first dealing with how temperature affects THOR (3), the second with how pathogenicity is related to competition ability in a community setting, the third about the genetic determinants of antibiotic susceptibility in Pseudomonas aeruginosa, the fourth about invasion with P. aeruginosa into THOR, and the last one is a proteomics study about one of the strongest hits in paper IV.

Emil has used a range of techniques, including traditional microbiological assays, transposon mutagenesis (INSeq), and proteomics, to identify genetic determinants of community stability and disruption. This has allowed him to explore how cooperative traits emerge and how pathogens like Pseudomonas aeruginosa interfere with community dynamics. His thesis can be found in an online version here.

References

1. 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
2. Burman E: Genetic Contributions to Invasion and Biofilm Disruption in a Microbial Model Community. PhD Thesis, University of Gothenburg (2025). https://gupea.ub.gu.se/handle/2077/87262
3. Burman E, Bengtsson-Palme J: Microbial community interactions are sensitive to small differences in temperature. Frontiers in Microbiology, 12, 672910 (2021). doi: 10.3389/fmicb.2021.672910

Over the last week, I have been featured in media in different ways, so here’s a quick summary.

I was asked to provide a comment on a recent paper on how microplastics affect antibiotic resistance development (1) for an article in Scientific American (2). I am not sure I had that much intelligent to say, other than to caution about jumping to conclusions, as we still know quite little about the risks associated with microplastics and AMR: “How much of a threat plastic-derived drug-resistant pathogens pose to humans is a question that remains to be fully understood” is one of my two quotes from the article.

I also was interviewed last week for Swedish Radio’s Vetenskapsradion (in Swedish) about another study showing that, e.g., ibuprofen could drive bacteria to higher mutation rates, indirectly triggering antibiotic resistance development (3). Such interaction effects have also been seen elsewhere (4), but the fact that they see this effect for such a commonly used drug as ibuprofen – one of our most standard painkillers – is a little bit concerning. Still I stress in the interview that we need to know much more about these interaction effects before jumping to clinical guidance.

Finally, the Foundation for Strategic Research has released the video they recorded about our research last fall. It is in Swedish, but with English subtitles, so this could be worth a watch!

References

1. Gross N, Muhvich J, Ching C, Gomez B, Horvath E,Nahum Y, Zaman MH: Effects of microplastic concentration, composition, and size on Escherichia coli biofilm-associated antimicrobial resistance. Appl Environ Microbiol, 91, e02282-24, (2025). https://doi.org/10.1128/aem.02282-24
2. Zaraska M: Microplastics Could Be Turning Bacteria into Drug-Resistant Superbugs. Scientific American, 2025-08-26. https://www.scientificamerican.com/article/microplastics-could-be-creating-dangerous-antibiotic-resistant-bacteria/
3. Chen H, Sapula SA, Turnidge J, et al.: The effect of commonly used non-antibiotic medications on antimicrobial resistance development in Escherichia coli. npj Antimicrob Resist 3, 73 (2025). https://doi.org/10.1038/s44259-025-00144-w
4. Maier L, Pruteanu M, Kuhn M, et al.: Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018). https://doi.org/10.1038/nature25979

This spring and summer have seen some changes to the composition of the research group, with people both coming and going. First of all, we have said goodbye to two postdocs who have worked in the lab for quite some time – Máté Vass and Daniel Jaén Luchoro. Máté is moving on to a position in Uppsala, at the Swedish University of Agriculture where he will start building up his own research group. Daniel is returning to a full time position at the Sahlgrenska Hospital, where he will keep doing part-time research. We look forward to keeping on working with both of them in their new roles!

Furthermore, we also say goodbye and thank for their wonderful contributions to the lab our two master students: Emilia Valfridsson and Felix Blomfelt. Both will be greatly missed, and they have made very valuable contributions to the group’s work, which (hopefully…) will result in publications relatively soon!

Finally, we would like to extend a somewhat belated welcome to our new postdoc Yuselys Garcia-Martinez who joined us in January. Yuselys will be working in the SEARCHER project on discovering novel antibiotic resistance genes in environmental and animal microbiomes.

On a personal note, this is the first time some of my long-term lab members leave the lab, so this feels especially sad to me. At the same time, they are moving on to new exciting roles, and maintaining and developing these relationships will be an interesting continuation of my journey as a group leader.

I am very happy to welcome Agata Marchi back to the group as a PhD student! Agata was a master student in the group last year, doing a thesis focused on implementing a bioinformatic approach to identify differences between the genomes of host-associated and non host-associated strains of Pseudomonas aeruginosa. While one of her first tasks will be to complete this work and prepare it for publication, her doctoral studies will primarily be on the interactions between bacteria and between bacteria and host in the human microbiome and how these relate to complex diseases. She will focus on developing and applying machine learning methods to better understand this interplay.

I am – as the rest of the group – very happy to welcome Agata back to the lab!

Time is passing quickly, and I have not appropriately acknowledged the many newcomers we’ve had to the lab in the past couple of months. With this post I would like to say welcome to the lab to Máté Vass and Dani Jáen Luchoro (both postdocs), Jorge Agramont and Josue Mamani Jarro (doctoral students), as well as Nathália Abichabki (visiting doctoral student from Brazil)! Some of you have already spent a couple of months in the group and we very much enjoy having you here!

A week or so ago, we took this new lab picture with everyone (except for Lisa, who is in Amsterdam). I am very proud to be working with group of extremely talented, smart, funny and goodhearted people!

Very briefly, Dani will be working on updating the BacMet database as part of the BIOCIDE project, and shares his time between my group, Joakim Larsson‘s group and the Sahlgrenska hospital. Máté was recruited within the DDLS program and will work on inferring the metacommunity ecology of antibiotic resistance based on analysis of large-scale datasets. Jorge and Josue are part of the same SIDA-funded doctoral student exchange program with Bolivia and will work on different aspects of environmental antibiotic resistance and the spread of diarrheal pathogens through the environmental matrix. Nathália, finally, is working on understanding the tolerance mechanisms to antibiotics in Klebsiella pneumoniae.

All of you are very welcome to the group!

Some good news from the lab! Emil Burman today passed his halftime control, which means that we now can look forward to around more years of fun science together! We all congratulate Emil on this great achievement which marks an important milestone in the group, as Emil is the first of the PhD students who have reached it to this point!

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!

I am extremely happy to share the news that the Swedish Foundation for Strategic Research has selected me as one of 16 young research leaders to receive their 15 million SEK grant awarded to give newly established researchers with high scientific and pedagogical competence the opportunity to develop as research leaders.

This grant is one of the more prestigious grants for young researchers in Sweden that I know of and I am very honored and thankful, both towards the foundation and my research group who have made this possible, to receive this grant. In combination with the DDLS funding from the Wallenberg Foundation, this will provide the lab with some very nice opportunities to explore more far-reaching endeavors in the next couple of years, which sets the stage for a very exciting half-decade to come!

Finally, I am also happy to see (after my ten-years old criticism of the gender distributions of these grants) that the distribution of grants this year was approximately gender-equal (seven out of 16 recipient were women). This is a good sign for both future Swedish research and the trustworthiness of these grants themselves.

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!