Tag: Environment

I have written an editorial piece for the Swedish Pathogens Portal in which I reflect a bit on the upcoming EU legislation requiring monitoring of AMR in major wastewater treatment plants (1). I also veer a bit into where environmental monitoring outside of sewage may play a role, using our review paper resulting from EMBARK as the starting point (2).

This is timed to coincide with the registration deadlines for two upcoming workshops on AMR surveillance in the environment; the first being the DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Disease on 7th-8th October in Uppsala, which I have been part of organising. The second is a workshop organised by CARe in Gothenburg on 28th October on the theme of sewage surveillance of antibiotic resistance, focusing on the new EU requirements.

My hope is that you will be a bit provoked by this and come to one of these workshops to discuss AMR surveillance and where to go next!

1. Bengtsson-Palme J: Surveillance of antimicrobial resistance – flying blind or flying behind? The Swedish Pathogens Portal, Editorial (2024). doi: 10.17044/scilifelab.27045433 [Link]
2. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 178, 108089 (2023). doi: 10.1016/j.envint.2023.108089 [Paper link]

Together with Anna Székely, I have been working on the organization of a DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases on October 7 – 8, in Uppsala.

The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches. We now invite submission of abstracts for short talks.

Deadline for abstract submission: 18 September 
Deadline to register to attend: 25 September –> REGISTER HERE! <– This includes abstract submission.

Link to more information and the PROGRAM

I hope to see all of you working with AMR in the environment in Uppsala in October!

Ákos Kovács had the brilliant idea of putting up a temporary resource for things you bring up in a talk that you can point people to. I did not do this before my talk at ISME today, but I thought the idea was so good, so here’s a summary and collection of my ISME short-talk on the EMBARK outcomes today:

• More information on EMBARK and its successor SEARCHER can be found on the project website, here: http://antimicrobialresistance.eu Importantly, this is a team effort over four years and I only touched on a few selected things
• Within the project we have looked at typical background levels of antibiotic resistance in the environment. We have already published some of these results (for qPCR abundances) in Abramova et al. 2023
• The average resistance gene in the average environment is present in ~1 in 1000 bacteria, but the variation between different genes is huge
• Depending on monitoring goal, different target genes are relevant to use. See this table adapted from Abramova et al. 2023:

• We have also tried to make different monitoring methods for environmental AMR comparable. Those mentioned in the talk were selective culturing for resistant bacteria, qPCR and shotgun metagenomics
• This data is not yet published, but overall we see relatively good correlation between qPCR and metagenomics. This is not true for all genes, though, and unfortunately neither qPCR nor metagenomics is always better than the other
• Culturing data is not very good at predicting specific antibiotic resistance gene abundances as the class level
• Finally, we have developed methods for discovering new types of ARGs, as seen in the ResFinderFG database: Gschwind et al. 2023
• We have also used these new methods to look at differences between established ARGs and latent ARGs in a variety of environments: Inda-Díaz et al. 2023
• Our ultimate goal in EMBARK would be to develop a modular framework for environmental monitoring of antibiotic resistance. You can read more about our thinking and goals in the review paper we published last year: Bengtsson-Palme et al. 2023

As part of the SEARCHER program, we are now hiring a two-year postdoc to work with innovative approaches to antibiotic resistance monitoring. You can read more about the position here and at Chalmers’ job portal, but in short we are after a wet-lab postdoc who are willing to do field work and laboratory studies to identify novel antibiotic resistance genes.

Please do not send me your CV and application letter via e-mail, but apply through the Chalmers application portal. Sending your CV to me will not increase your changes. Only contact me about this position if you have actual, relevant questions about the position (as I will otherwise get lots of unwanted e-mails…) Those questions, I am happy to answer!

On the 5th and 6th of October this year, I will be taking part in a relatively small, but very interesting conference on veterinary and environmental AMR, held in Amsterdam. The theme of the event will be “Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain”.

The aim of the conference is to discuss innovative additional measures to prevent development of resistance in animals. In addition, the participants will explore possibilities to prevent transfer to human health care after selection has taken place. The conference program will consist of both lectures and break-out sessions and is intended for researchers as well as for policy makers involved in the battle against antimicrobial resistance. The results of the break-out sessions are to be published in an open access journal, and I will be charing one of these break-out sessions. Please see the conference web site for the entire program: https://www.nvwa.nl/amrconference

There is an upper cap of 120 participants for the event, so if you’re interested make sure to register soon! The conference will be held on October 5 and 6 2023 in the Park Inn by Radisson in Amsterdam, The Netherlands. The hotel is easy to reach by a 12 minutes train ride from Schiphol airport and a 5 minutes train ride from the city center. 

I look forward to seeing you in Amsterdam!

In just a few days, Environment International has published two papers coming out from the EMBARK consortium which are somewhat connected to each other.

The first (or technically the second, but the other order makes more sense when explaining this…) is the first paper involving most of the people who have been working in the EMBARK consortium for an extended period of time. It’s an overview paper titled “Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement Itit, and what are the data needs?” (1) and I think the title describes the topic pretty well. Basically, we go through why it would be interesting to monitor for antibiotic resistance in the environments, how that could be implemented and what we would need to know to get there.

The very condensed story is that if one is considering implementing monitoring for environmental resistance, these are a few things that should be considered:

• The purpose of monitoring: What is the motivation? What should be achieved? What type of risk should be assessed? What type of action would monitoring enable?
• Choice of methods: Which methods are economically feasible? Which methods would deliver results within a useful timeframe for taking appropriate actions?
• Targeted environments: In what type of environment would monitoring for a given purpose be worthwhile?
• Intended users: Who would be able to use, implement and act upon this strategy?
• Integration potential: How does this monitoring integrate with other monitoring efforts? How can the resulting data be communicated?

We then dive into the knowledge gaps we are currently facing, and particularly highlight the following areas:

• Establish how different existing methods for monitoring resistance compare to each other
• Extend pathogen-centric databases for resistance genes with latent resistance genes (2)
• Determine the locations and type of environments relevant for resistance monitoring
  To reduce costs, utilizing already existing environmental monitoring should be prioritized, as should locations integrated into operating or planned surveillance programs. More efforts should also be made to identify additional pathways for resistance transmission through the environment.
• Study the environment as a source and transmission route for antibiotic resistance
  Stratify risks associated with resistance genes found in the environment. Define typical levels of antibiotic resistance in different environments (3), and define how these levels change over time.
• Identify settings where the relationship between fecal bacteria and antibiotic resistance is absent
  Usually, these levels follow each other, but the environments where they don’t are important as they deviate from the expected baseline of resistance. This knowledge can aid in identifying situations in which it would be helpful to investigate a microbial community for resistance to specific antibiotics.
• Identify the origins for more antibiotic resistance genes (4)
  This knowledge will be instrumental in preventing the emergence of new forms of resistance in pathogens in the future.

An important outcome of this paper is that we realise that we are still not at a level of understanding where routine monitoring for resistance in the environment can be easily justified or implemented. Still, there is a need for monitoring data in natural environments to even get started, and therefore we support the implementation of national, regional and global of initiatives without having all the scientific answers. The lack of comprehensive understanding should not be an obstacle to starting environmental monitoring for AMR, nor for action against environmental development and spread of AMR.

The second paper is very much related to the first, in that it actually tries to address one of these knowledge gaps: the need for normal background levels of antibiotic resistance in different environments. In this paper, Anna Abramova did an herculean effort collecting (we hope) all qPCR data on antibiotic resistance gene abundances in the environment for the past two decades. All in all, she collected data for more than 1500 samples across 150 studies and integrated these into an analys of what we could consider normal levels of resistance in different environments.

For an ‘average’ resistance gene, we found that the normal relative abundance range was form 10^-5 to 10^-3 copies per bacterial 16S rRNA, or that around one in 1,000 bacteria would carry a given resistance gene. This level varied quite a bit between different resistance genes, however, but not so much between environmental types (except for in human and animal feces, where some resistance genes were clearly more abundant, most prominently tetracycline resistance genes). What was more striking was that there was a clear difference between environments impacted or likely impacted by human activities, as opposed to more pristine environments with little to none human impact. Some resistance genes, such as tetA, tetG, blaTEM and blaCTX-M, showed very marked differences between these impacted and non-impacted environments, making them great markers of human-activity-associated resistance.

Our final recommendations with regards to monitoring include:

• Include the intI1, sul1, blaTEM, blaCTX-M and qnrS genes in environmental monitoring, along with a selection of tetracycline resistance genes, including either tetA or tetG.
• Other potential target genes could be sul3, vanA, tetH, aadA2, floR, ereA and mexF, which are abundant in some environments, but are not often included in qPCR studies of environmental AMR
• If a gene deviates from the expected 10^-5 to 10^-3 interval, this warrants further investigation of the causes.
• Maximum acceptable levels need to be determined not only taking relative abundances of genes into account, but also risks to human health as well as the numbers of bacteria in a given volume of sample into account (5,6) and transmission routes to humans (7)
• The different standards of reporting DNA abundances constituted a complicating factor for this study. Both abundances of resistance genes relative to the 16S rRNA gene and to the sample volume or weight should be reported.
• The absence of clear trends of increases or decreases in resistance gene abundances over time indicates a need for more systematic time series data in a variety of environments.

Our results also highlighted the scarcity of resistance gene data from parts of the world, particularly from Africa and South America, and underscores the need for a concerted effort to quantify typical background levels of resistance in the environment more broadly to enable efficient environmental surveillance schemes akin to those that exist in clinical and veterinary settings.

I encourage anyone with an interesting these topics to at least skim the full papers [Monitoring overview paper here, Normal qPCR resistance abundances here]. These will be great resources and I am very proud of them both. I would really like to thank the entire EMBARK team and our collaborators in CORNELIA, WastPAN and in other organisations. I would also like to thank Anna for her hard work on collecting and analysing the qPCR data for around two years. It has been a long ride, and I think we are both happy, proud and a bit relieved to finally see this paper published!

References

1. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 108089 (2023). doi: 10.1016/j.envint.2023.108089
2. Inda-Díaz JS, Lund D, Parras-Moltó M, Johnning A, Bengtsson-Palme J, Kristiansson E: Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. Microbiome, 11, 44 (2023). doi: 10.1186/s40168-023-01479-0
3. Abramova A, Berendonk TU, Bengtsson-Palme J: A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments. Environment International, 178, 108084 (2023). doi: 10.1016/j.envint.2023.108084
4. Ebmeyer S, Kristiansson E, Larsson DGJ: A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology, 4 (2021). doi:10.1038/s42003-020-01545-5
5. Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018). doi: 10.1016/j.envint.2018.04.041
6. Pruden A, Larsson DGJ, Amézquita A, Collignon P, Brandt KK, Graham DW, et al. Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environmental Health Perspectives, 121, 878–885 (2013). doi:10.1289/ehp.1206446
7. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053

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.

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Last week, a paper resulting from a collaboration with Stefanie Heß and Viktor Jonsson was published in Environmental Science & Technology. In the paper, we build a quantitative model for the emergence of antibiotic resistance genes in human pathogens and populate it using the few numbers that are available on different processes (bacterial uptake, horizontal gene transfer rates, rate of mobilization of chromosomal genes, etc.) in the literature (1).

In short, we find that in order for the environment to play an important role in the appearance of novel resistance genes in pathogens, there needs to be a substantial flow of bacteria from the environment to the human microbiome. We also find that most likely the majority of resistance genes in human pathogens have very small fitness costs associated with them, if any cost at all.

The model makes three important predictions:

1. The majority of ARGs present in pathogens today should have very limited effects on fitness. The model caps the average fitness impact for ARGs currently present in human pathogens between −0.2 and +0.1% per generation. By determining the fitness effects of carrying individual ARGs in their current hosts, this prediction could be experimentally tested.
2. The most likely location of ARGs 70 years ago would have been in human-associated bacteria. By tracking ARGs currently present in human pathogens across bacterial genomes, it may be possible to trace the evolutionary history of these genes and thereby identify their likely hosts at the beginning of the antibiotic era, similar to what was done by Stefan Ebmeyer and his colleagues (2). What they found sort-of corroborate the findings of our model and lend support to the idea that most ARGs may not originate in the environment. However, this analysis is complicated by the biased sampling of fully sequenced bacterial genomes, most of which originate from human specimens. That said, the rapid increase in sequencing capacity may make full-scale analysis of ARG origins using genomic data possible in the near future, which would enable testing of this prediction of the model.
3. If the origins of ARGs currently circulating in pathogens can be established, the range of reasonable dispersal ability levels from the environment to pathogens narrows dramatically. Similarly, if the rates of mobilization and horizontal transfer of resistance genes could be better determined by experiments, the model would predict the likely origins more precisely. Just establishing a ball-park range for the mobilization rate would dramatically restrict the possible outcomes of the model. Thus, a more precise determination of any of these parameters would enable several more specific predictions by the model.

This paper has a quite interesting backstory, beginning with me having leftover time on a bus ride in Madison (WI), thinking about whether you could quantize the conceptual framework for resistance gene emergence we described in our 2018 review paper in FEMS Reviews Microbiology (3). This spurred the first attempt at such a model, which then led to Stefanie Heß and me applying for support from the Centre for Antibiotic Resistance Research at the University of Gothenburg (CARe) to develop this idea further. We got this support and Stefanie spent a few days with me in Gothenburg developing this idea into a model we could implement in R.

However, at that point we realized we needed more modeling expertise and brought in Viktor Jonsson to make sure the model was robust. From there, it took us about 1.5 years to refine and rerun the model about a million times… By the early spring this year, we had a reasonable model that we could write a manuscript around, and this is what now is published. It’s been an interesting and very nice ride together with Stefanie and Viktor!

References

1. Bengtsson-Palme J, Jonsson V, Heß S: What is the role of the environment in the emergence of novel antibiotic resistance genes? A modelling approach. Environmental Science & Technology, Article ASAP (2021). doi: 10.1021/acs.est.1c02977 [Paper link]
2. Ebmeyer S, Kristiansson E, Larsson DGJ: A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology 4 (2021). doi: 10.1038/s42003-020-01545-5
3. Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053 [Paper link]

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!

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!