Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg

Browsing Posts tagged Public information

In two weeks time, on the 15th of June, I will participate in a seminar organised by Landstingens nätverk för läkemedel och miljö (the Swedish county council network for pharmaceuticals and environment; the seminar will be held in Swedish) in Stockholm. I will give a talk on our proposed emission limits for antibiotics published last year (the paper is available here), but there will also be talks on wastewater treatment, sustainable pharmaceutical usage and environmental standards for pharmaceuticals. The full program can be found here, and you may register here until June 9. The seminar is free of charge.

And if you are interested in this, I can also recommend the webinar given by Healthcare Without Harm next week (on June 8), which will deal with sustainable procurement as a means to deal with pharmaceutical pollution in the environment. I will at least tune in to hear how the discussion goes here.

First of all, I am happy to announce that the webinar I participated in on the (un)recognised pathways of AMR: Air pollution and food, organised by Healthcare Without Harm is now put online so that you can view it, in case you missed out on this event. To be honest it is probably not one of my best public appearances, but the topic is highly interesting.

Second, next week I am taking part in Vetenskapsfestivalen – the Science Festival in Gothenburg. Specifically, I will be on of the researchers participating in the Science Roulette, taking place in the big ferris wheel at Liseberg. This will take place between 17.00 and 18.00 on May 11th. The idea is that people will be paired with researchers in diverse subjects, of which I am one, and then have a 20 minute chat while the wheel is spinning. Sounds like potential for lot of fun, and I hope to see you there! I will discuss antibiotic resistance, and for how much longer we can trust that our antibiotics will work.

So, on Thursday (May 26th) I will defend my thesis, titled “Antibiotic resistance in the environment: a contribution from metagenomic studies”. I will not dwell into this by writing a novel text, but will instead shamelessly reproduce the press release, which should give a reasonable overview of what I have been doing:

More and more people are infected with antibiotic resistant bacteria. But how do bacteria become resistant? A doctoral thesis from the Centre for Antibiotic Resistance Research at University of Gothenburg has investigated the role of the environment in the development of antibiotic resistance.

“An important question we asked was how low concentrations of antibiotics that can favour the growth of resistant bacteria in the environment”, says Johan Bengtsson-Palme, author of the thesis.

“Based on our analyses, we propose emission limits for 111 antibiotics that should not be exceeded in order to avoid that environmental bacteria become more resistant.”

A starting point to regulate antibiotic pollution
A recent report, commissioned by the British Prime Minister David Cameron, proposes that the emission limits suggested in Johan’s thesis should be used as a starting point to regulate antibiotic pollution from, for example, pharmaceutical production – globally.

“Many people are surprised that such regulations are not already in place, but today it is actually not a crime to discharge wastewater contaminated with large amounts of antibiotics, not even in Europe”, says Johan Bengtsson-Palme.

Resistance genes
In one of the studies in the thesis, the researchers show that resistance genes against a vast range of antibiotics are enriched in an Indian lake polluted by dumping of wastewater from pharmaceutical production.

“It’s scary. Not only do the bacteria carry a multitude of resistance genes. They are also unusually well adapted to share those genes with other bacteria. If a disease-causing bacterium ends up in the lake, it may quickly pick up the genes it needs to become resistant. Since the lake is located close to residential areas, such spread of resistant bacteria to humans is not hard to imagine”, says Johan Bengtsson-Palme.

Spreading by travelers
The thesis also shows that resistant bacteria spread in the intestines of travelers who have visited India or Central Africa, even if the travelers themselves have not become sick.

“That resistant bacteria spread so quickly across the planet highlights that we must adopt a global perspective on the resistance problem”, says Johan Bengtsson-Palme. “Furthermore, it is not enough to reduce the use of antibiotics in healthcare. We must also reduce the use of antibiotics for animals, and try to limit the releases of antibiotics into the environment to try to get control over the growing antibiotic resistance problem before it is too late”.

The thesis Antibiotic resistance in the environment: a contribution from metagenomic studies will be defended on a dissertation on May 26th.

UPDATE: This post has been updated to reflect a valid comment that I messed up in the original post. Specific use of antibiotics as feed additives has been forbidden for years in the EU. The petition was about cutting the prophylactic use of antibiotics in animals, but that was very unclear from the original post. I thank my readers for pointing this unclarity out.

I’m going to do something unusual and ask you to sign a petition targeted at European Union ministers to support new EU laws to drastically cut the prophylactic use of antibiotics in agriculture as growth promoters. The problem is that if ministers don’t feel the public pressure to act, the laws may be delayed or not be implemented. Examples from Denmark, Sweden, Norway and the Netherlands show that it is possible to produce meat with little or no antibiotics, but since bacteria can travel across borders (1), we need to bring the rest of the world onboard, and the EU is good first step. Therefore I ask you to sign the Avaaz petition here.

  1. Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551-6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]

The paper we published in August on travelers carrying resistance genes with them in their gut microbiota has now been typeset and got proper volume and issue numbers assigned to it in Antimicrobial Agents and Chemotherapy. Take a look at it, I personally think it’s quite good-looking.

Also, if you understand Swedish, here is an interview with me broadcasted on Swedish Radio last month about this study and the consequences of it.

The new citation for the paper is:

  • Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551-6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]

There have been quite a lot of buzz this week around the travel paper we published earlier this month. Twitter aside, the findings of the paper has also been covered by a range of news outlets, both in Sweden and internationally. Today, I was on Swedish radio talking resistance problems for about ten minutes (listen here; in Swedish). Here’s a few takes on the story I gathered around the web:

Science Daily
Business Standard
Z News
Englemed Health News
Läkemedelsvärlden (in Swedish)
Sveriges Radio (in Swedish)
Göteborgs-Posten (in Swedish)

A couple of days ago a paper was published in Environmental Sciences Europe summarizing the EU report on effect-based tools for use in toxicology in the aquatic environment I have been involved in (1). This report was officially published last spring (2), and can be found here, with the annex available on the European Commission document website. My contribution to the paper was, as with the report, in the genomics and metagenomics section. The paper briefly presents modern bioassays, biomarkers and ecological methods that can be used for aquatic monitoring of the environment.

References:

  1. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Dulio V, Broeg K, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, O’Toole S, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Hollert H, Di Paolo C, Brack W. Kammann U, Kase R: The European technical report on aquatic effect-based monitoring tools under the water framework directive. Environmental Sciences Europe, 27, 7 (2015). doi: 10.1186/s12302-015-0039-4 [Paper link]
  2. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Broeg K, Kammann U, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kase R, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Dulio V, Hollert H, Di Paolo C, Brack W (2014). Technical Report on Aquatic Effect-Based Monitoring Tools. European Commission. Technical Report 2014-077, Office for Official Publications of European Communities, ISBN: 978-92-79-35787-9. doi:10.2779/7260

My colleague Henrik Nilsson has been interviewed by the ResearchGate news team about the recent effort to better annotate ITS data for plant pathogenic fungi. It’s an interesting read, and I think Henrik nicely underscores why large-scale efforts for improving and correcting sequence annotations are important. You can read the interview here, and the paper they talk about is referenced below.

Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F, Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson K-H, Kõljalg U, Abarenkov K: Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, Volume 67, Issue 1 (2014), 11–19. doi: 10.1007/s13225-014-0291-8 [Paper link]

Because of my previous involvement in a Swedish report on toxicological monitoring using (meta)-genomics tools [1], I also became in a related EU report on effect-based tools for use in toxicology in the aquatic environment. This report has recently been officially published [2], and can be found here, with the annex available on the European Commission document website. My contribution to this report has been in the genomics and metagenomics section (Chapter 7: OMICS techniques), in which I wrote the metagenomics part and contributed to the rest. I personally think this is a quite forward-thinking report, which is nice for a large institution such as the EU.

  1. Länsstyrelsen i Västra Götalands län. (2012). Swedish monitoring of hazardous substances in the aquatic environment (No. 2012:23). (A.-S. Wernersson, Ed.) Current vs required monitoring and potential developments (pp. 1–291). Länsstyrelsen i Västra Götalands län, vattenvårdsenheten.
  2. Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Broeg K, Kammann U, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kase R, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Dulio V, Hollert H, Di Paolo C, Brack W (2014). Technical Report on Aquatic Effect-Based Monitoring Tools. European Commission. Technical Report 2014-077, Office for Official Publications of European Communities, ISBN: 978-92-79-35787-9. doi:10.2779/7260

A poor excuse…

Comments off

I feel very sorry that I have been a little bit unresponsive for the last couple of weeks. I have received several questions regarding the PETKit and ITSx that i have not yet got around to answer. I am very sorry for that inconvenience. The reason (not a good excuse, but still) is that I have been overloaded with grant applications. This will continue through the rest of september, so please be patient until October if I don’t reply e-mails. If you need a quick response, please state so very clearly, and I might be able to squeeze you in before the start of October. Otherwise, see you at the other end of the tunnel! Thanks for the understanding.