Tag: Antibiotics

Funding from the research council!

I am very happy to share the news that our starting grant application to the Swedish Research Council has been granted 3.3 million SEK of funding for four years! This is fantastic news, as it allows us to further explore the interactions between bacteria in the human microbiome that are important for community stability and resilience to being colonized by pathogens. In the granted project, we will investigate environmental and genetic factors that are important for bacterial invasiveness and community stability in the human gastrointestinal tract.

Within the scope of the project, we will establish model bacterial communities and experimental systems for the human stomach and intestine. We will then investigate how disturbances, such as antibiotic exposure, change the interactions in these microbial communities and their long-term stability. Finally, we aim to identify genes that contribute to successful bacterial colonization or resilience to invasion of established communities in the human microbiome.

Aside from myself, Prof. Sara Lindén and Dr. Kaisa Thorell from the University of Gothenburg as well as Prof. Ed Moore at the university’s Culture Collection will be involved in this project in different ways. We will also collaborate with my former postdoc supervisor Prof. Jo Handelsman as well as Dr. Ophelia Venturelli at the University of Wisconsin-Madison. Finally, we will also collaborate with Dr. Åsa Sjöling at the Karolinska Institute. I look forward to work with you all over the coming four years! A big thanks to the Swedish Research Council for believing in this research and investing in making it happen!

The Gothenburg Society of Medicine’s research prize

I am very happy to share the news that I have been awarded with the Gothenburg Society of Medicine and the Sahlgrenska Academy’s prize to young researchers for our research on the effects of antibiotics on bacteria, including, of course, antibiotic resistance.

I am incredibly honoured by being selected for this award. I am also thrilled with that the Gothenburg Society of Medicine, which is a society mostly for medical doctors, sees the value in our broad, one-health, take on antibiotic resistance as well as other effect that antibiotics may have on microbes, both in the human body and in the environment. The recognition of antibiotic resistance as a one-health problem with solutions both within and outside of the typical medical setting is instrumental for our ability to curb future resistance development.

The award ceremony will take place in connection with the Gothenburg Society of Medicine’s closing meeting on 2 December, where I will present our research together with the senior awardee Professor Claes Ohlsson, who is awarded for his groundbreaking research on osteoporosis.

EFSA Public Consultation

For a bit more than a year, I have been part of an EFSA panel on biological hazards on cross contamination with antibiotic substances in animal feed. This week the panel has launched an open consultation on sections of the draft scientific opinion, including the proposed methodology and the data gaps identified. Anyone who are interested can submit written comments before 18 November 2020, and the full information can be found at the EFSA website.

Open postdoc position

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.

EMBARK funded by JPIAMR

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!

Open PhD position

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.

Published book chapter: Reducing resistance in the environment

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]

Thank you Alice!

This week marked the departure of our summer internship student Alice Zublena, who is now heading back to France to finish her masters program. Alice has been working on establishing effect concentrations for beta-lactam antibiotics for different bacteria, and has generated a very exciting and useful data set for our work in the coming years. I am tremendously happy that I have got to work with Alice this summer and very thankful for having the opportunity to supervise such a talented student. Thanks for your great work this summer Alice and good luck with everything you pursue in the future! 

Published paper: Increased antibiotic resistance in Croatian pharmaceutical wastewater treatment plant

I celebrate the fourth of July with the coincidental publishing of my most recent paper, in collaboration with the lab of Nikolina Udikovic-Kolic. The study used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin (1). We compared the levels of antibiotic resistance genes in sludge from this treatment plant and municipal sludge from a sewage treatment plant in Zagreb, and found that the total abundance of resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production. To our great surprise, this was not true for macrolide resistance genes, however. Instead, those genes had overall slightly lower abundances in the industrial sludge. At the same time, the genes that are associated with mobile genetic elements (such as integrons) had higher abundances in the industrial sludge.

This leads us to think that at high concentrations of antibiotics (such as in the industrial wastewater treatment plant), selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance genes. Unfortunately, the results regarding resistance mutation – obtained using our recent software tool Mumame (2) – were uninformative due to low number of reads mapping to the resistance regions of the 23S rRNA target gene for azithromycin.

Often, the problem of environmental pollution with pharmaceuticals is perceived as primarily being a concern in countries with poor pollution control, since price pressure has led to outsourcing of global antibiotics production to locations with lax environmental regulation (3). If this was the case, there would be much less incentive for improving legislation regarding emissions from pharmaceutical manufacturing at the EU level, as this would not move the needle in a significant way. However, the results of the paper (and other work by Nikolina’s group (4,5)) underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.

References

  1. 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, accepted manuscript (2019). doi: 10.1016/j.watres.2019.06.073
  2. Magesh S, Jonsson V, Bengtsson-Palme JQuantifying point-mutations in metagenomic data. bioRxiv, 438572 (2018). doi: 10.1101/438572
  3. Bengtsson-Palme J, Gunnarsson L, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? Journal of Cleaner Production, 171, 137–146 (2018). doi: 10.1016/j.jclepro.2017.09.247
  4. Bielen A, Šimatović A, Kosić-Vukšić J, Senta I, Ahel M, Babić S, Jurina T, González-Plaza JJ, Milaković M, Udiković-Kolić N: Negative environmental impacts of antibiotic-contaminated effluents from pharmaceutical industries. Water Research, 126, 79–87 (2017). doi: 10.1016/j.watres.2017.09.019
  5. González-Plaza JJ, Šimatović A, Milaković M, Bielen A, Wichmann F, Udikovic-Kolic N: Functional repertoire of antibiotic resistance genes in antibiotic manufacturing effluents and receiving freshwater sediments. Frontiers in Microbiology, 8, 2675 (2017). doi: 10.3389/fmicb.2017.02675


The Lennart Sparell Prize

I am happy to announce that Cancer- och Allergifonden [the Cancer and Allergy Foundation] have awarded me with the first Lennart Sparell prize. The prize was instated in memory of the foundations founder – Lennart Sparell, who passed away last year – and is awarded to researchers (or other persons) who have thought outside-of-the-box or challenged the current paradigms. A particular emphasis is given to research on environmental pollutants that affect human health through food or environmental exposure.

Naturally, I am honored to be the recipient of this prize. The award was motivated by the research I have done on the role of ecological and evolutionary processes in the external environment in driving antibiotic resistance development, and how that can have consequences for human health. Particularly, I am happy that the research that I, Joakim Larsson, Erik Kristiansson and a few others on the role of environmental processes in the development of antibiotic resistance and the recruitment of novel resistance genes are given attention. This view, which perhaps do not challenge the paradigm but at the very least points to an alternative risk scenario, has often been neglected when environmental antibiotic resistance has been discussed.

The prize will be awarded on a ceremony on June 10 in Stockholm, but I would already now take the opportunity to thank everyone who has been involved in the research being recognized, particularly Joakim Larsson and Erik Kristiansson – this award is to a very very large extent to your merit.