We have been awarded with the first best article award from FEMS Microbiology Reviews for our 2018 review Environmental factors influencing the development and spread of antibiotic resistance. I and my co-authors Joakim Larsson and Erik Kristiansson are honoured and – of course – very happy with this recognition of our work. I was interviewed in relation to the prize, an interview that can be read here. But, also, the paper is open access, so you can go and check it all out in its full glory right now!

We are hiring a postdoc to work with environmental monitoring of antimicrobial resistance. The project is part of the EMBARK program and will consider different aspects of establishing a baseline for background antibiotic resistance in the environment, standardization of monitoring protocols and development of methods to detect emerging resistance threats. The project will involve work with environmental sampling, DNA extractions, bacterial culturing and generation of large-scale DNA sequence data. In terms of bioinformatic analyses, the project will encompass analysis of next-generation sequence data, genome-resolved metagenomics, short-read assembly and network analysis.

We look for a skilled bioinformatician, preferably with experience of experimental laboratory work. If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is January 3.

I just wanted to very quickly brief applicants to the recently announced PhD position in the lab. We got 71 applications in total, most of which I consider relevant for the position. The bottom line is that this will take a few days to go through, but we are working on it, and will get in touch with the top candidates when we are done. I would, however, already like to thank everyone who applied – it’s amazing that you want to spend your time doing research that I find exiting!

I am very happy to announce today (on the European Antibiotic Awareness Day), that the EMBARK project that I am coordinator for got funded by JPIAMR with almost 1.4 million Euros over three years!

The primary goal of EMBARK is to establish a baseline for how common resistance is in the environment and what resistance types that can be expected where. That background data will then underpin efforts to standardize different methods for resistance surveillance and identify high-priority targets that should be used for efficient monitoring. In addition, EMBARK will develop and evaluate methods to detect new resistance factors and thereby provide an early-warning system for emerging resistance threats.

EMBARK is an international collaboration funded by JPIAMR. The consortium consists of myself, Thomas Berendonk (TU-Dresden, Germany), Luis Pedro Coelho (Fudan University, China), Sofia Forslund (ECRC Max-Delbrück-Centrum für Molekulare Medizin, Germany), Etienne Ruppé (INSERM, France) and Rabaab Zahra (Quaid-i-Azam University, Pakistan).

EMBARK has a website where the protocols and data generated during the project will be released. Follow our progress towards better monitoring of antimicrobial resistance in the environment here and on the EMBARK Twitter account: @EMBARK_JPIAMR!

We are hiring a PhD student to work with effects of antibiotics on microbial communities! The project will use large-scale techniques to investigate how sub-inhibitory concentrations of antibiotics affect microbial communities. Specifically, the project will examine how the ability for bacteria to colonize and invade established microbial communities is impacted by antibiotics. The project will also explore how antibiotics influence the interactions between different species in bacterial communities and if this may change their ability to withstand invasions. The goal is to identify the genes and mechanisms that contribute to change and stability in microbial communities.

A cool thing about this position is that it is fairly adaptable to the eventual candidate, and the project can be somewhat tailored to suit the profile of the PhD student. This means that we’re looking for someone who is either a bioinformatician or an experimentalist (or both). Previous experience with microbial communities is a plus, but not a must.

If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is December 9.

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!

ITSx has been updated with some minor bug fixes (solving bugs that caused big problems for a small subset of users).

The first bug was that the no detections file generated in a previous file was not removed before it was written to (if it happened to have the same name in a subsequent run). This could cause weird errors where sequences which were not part of the input file were reported as not detected, and subsequently inconsistent counts for the number of missing sequences. This bug should now be fixed (although I have to admit that it is hard to test for this error in all possible scenarios).

The second bug was very serious for anyone who worked with ITS sequences from Chlorophyta. The ‘-t’ option did not accept ‘G’ (the code for Chlorophyta) as an option, while it did accept ‘green algae’ or ‘chlorophyta’. The Chlorophyta profiles were also included in the default ‘all’ profiles mode, and thus this error did not manifest itself for the vast majority of users. I am sorry for the mess this must have caused for the Chlorophyta researchers using ITSx and thank the users of the software for pointing this error out.

Sorry for these bug fixes taking so long! It has been a very unusual and stressful spring and summer, and I hope to be able to be more responsive in the future. The new update brings ITSx to version 1.1.2. No other changes except the two bug fixes have been made in this version.

The shift to October marked the last days that our visiting doctoral student Adriana Osińska spent in the lab. Adriana was working on the sequencing data generated from the invasion experiments I performed in Jo Handelsman’s lab. She managed to dig out a great number of genes that seems to have an influence on bacterial community invasion success. Those genes are now candidate genes that will be tested in follow-up studies, which brings us to….

That I forgot to introduce our newest lab member – Emil Burman! Emil is a master student performing his thesis project in the lab and will stay with us until May 2020. Emil will work on experimentally characterizing the candidate genes that Adriana has identified. We are excited to have Emil in the lab and think that he has been off to a great start already. Welcome Emil!

Adriana will no go back to Poland to complete here PhD thesis early next year. We have loved to have her in the lab and she has contributed with data and analyses of tremendous value. We wish her all the best of luck with defending her thesis!

I have been slow at picking this ball up, but the book chapter that I coauthored with Stefanie Hess is now available online (and has been for almost a month). It is part of the book Antibiotic Drug Resistance, edited by José-Luis Capelo-Martínez and Gilberto Igrejas and was available in print on September 9th.

Our chapter deals with sources of resistant bacteria to the environment, and in particular the roles of sewage, wastewater and agriculture in resistance dissemination. Furthermore, the chapter discusses de novo selection of resistance and defines relevant risk scenarios. Finally, we outline the different management options available and discuss their feasibility.

The chapter boils down to that the available strategies for limiting antibiotic resistance dissemination and selection in the environment are overall quite clear. Larger problems that remain to be solved are how to prioritize between different strategies, which technologies that would provide the largest benefits and to achieve the political willingness to pursue these strategies. We note that several of the most efficient resistance prevention options involve high costs, investments in technology and infrastructure in other countries or proposals that are likely to be rather unpopular with the general public. For example, investing in sewage treatment and water infrastructure in low-income countries would likely be among the most effective means to reduce releases of resistant bacteria into the environment and reduced meat consumption would contribute to lower the use of antibiotics in animal husbandry, but neither is a very popular proposal for tax payers in high-income countries.

I have not yet read the entire book myself, but the table of content shows a very wide-reaching and comprehensive picture of the antibiotic resistance field, with a range of prominent authors. The editors have made a good job collecting this many interesting book chapters in the same volume!

Reference

Bengtsson-Palme J, Heß S: Strategies to reduce or eliminate resistant pathogens in the environment. In: Capelo Martinez JL, Igrejas G (Eds.) Antibiotic Drug Resistance, 637–673. Wiley, NJ, USA (2020). doi: 10.1002/9781119282549.ch24[Link]

I am happy to share the news that the paper describing out software tool Mumame is now out in its final form! (1) The paper got published today in the journal Metabarcoding and Metagenomics after being available as a preprint (2) since last autumn. This version has not changed a whole lot since the preprint, but it is more polished and better argued (thanks to a great review process). The software is virtually the same, but is not also available via Conda.

In the paper, we describe the Mumame software, which can be used to distinguish between wildtype and mutated sequences in shotgun metagenomic sequencing data and quantify their relative abundances. We further demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets (3-6), and find that the tool is useful but that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than is needed for most other applications of shotgun metagenomics. Since the preprint was published, Mumame has also found use in our recently published paper on selection for antibiotic resistance in a Croatian macrolide production wastewater treatment plant, unfortunately with inconclusive results (7). Mumame is freely available here.

I again want to stress the fantastic work that Shruthi Magesh did last year as a summer student at WID in the evaluation of this tool. As I have pointed out earlier, I did write the code for the software (with a lot of input from Viktor Jonsson), but Shruthi did the software testing and evaluations. Thanks and congratulations Shruthi, and good luck in pursuing your PhD program!

References

1. Magesh S, Jonsson V, Bengtsson-Palme J: Mumame: A software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics, 3: 59–67 (2019). doi: 10.3897/mbmg.3.36236
2. Magesh S, Jonsson V, Bengtsson-Palme J: Quantifying point-mutations in metagenomic data. bioRxiv, 438572 (2018). doi: 10.1101/438572
3. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648
4. Lundström S, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Science of the Total Environment, 553, 587–595 (2016). doi: 10.1016/j.scitotenv.2016.02.103
5. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: The structure and diversity of human, animal and environmental resistomes. Microbiome, 4, 54 (2016). doi: 10.1186/s40168-016-0199-5
6. Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ: Selective concentration for ciprofloxacin in Escherichia coli grown in complex aquatic bacterial biofilms. Environment International, 116, 255–268 (2018). doi: 10.1016/j.envint.2018.04.029
7. Bengtsson-Palme J, Milakovic M, Švecová H, Ganjto M, Jonsson V, Grabic R, Udiković Kolić N: Pharmaceutical wastewater treatment plant enriches resistance genes and alter the structure of microbial communities. Water Research, 162, 437-445 (2019). doi: 10.1016/j.watres.2019.06.073