Pandemic Preparedness Portal
I am happy to announce that I am joining the editorial committee of the Swedish Pandemic Preparedness Data Portal (formerly the Swedish COVID-19 portal). I will join five other researchers associated with SciLifeLab and will work together with the portal team to maximise the utility of the Portal for researchers, expand its content beyond SARS-CoV-2, and increase engagement with the research community. My main responsibility areas will be antibiotic resistance and emerging pathogens.
Since 2022 the portal is part of the SciLifeLab Pandemic Laboratory Preparedness (PLP) Program. It is operated by the SciLifeLab Data Centre. Over time, the popularity of the Portal has increased within the research community, the general public, and those involved in healthcare, industry, and policy making. I very much look forward to work with Luisa Hugerth (Uppsala University), Laura Carroll (Umeå University), Benjamin Murrell (Karolinska Institute), Mahmoud Naguib (Uppsala University) and Johan Ankarklev (Stockholm University) on the future of the portal!
20 positions for data scientists
I thought this could be interesting to some. SciLifeLab has opened 20 permanent staff positions for the new Data platform and Data Science Nodes (DSNs) organised within the DDLS program (that also funds my current position). These can be exciting opportunities to work with big data for someone who might not want to climb the academic group leader career ladder. The positions are spread out over Stockholm, Uppsala, Gothenburg and Linköping and can be found here.
BIG NEWS: We’re moving to Chalmers
I have very big and exciting news to share with you. After more than 10 years at the Sahlgrenska Academy, me and my lab will be moving from the University of Gothenburg to Chalmers University of Technology (which is physically a move of less than a kilometer, so still within Gothenburg). I have been offered a position at the Division of Systems Biology, funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS). The total funding to my lab will be 17 million SEK, with some co-funding from Chalmers added in on top of that.
I am of course very excited about this opportunity, which will bring some infrastructure that we need in-house that we don’t have easy access to today. At the same time, I am sad to leave my academic ‘home’, and the fantastic people we have been working with there for the years. I am also endlessly thankful for the support and trust that the Sahlgrenska Academy, the Institute of Biomedicine and the Department of Infectious Diseases have put into me and my research over the past years.
The transition to Chalmers will start already in May, but will be gradual and continue for a long time. We have close ties to the Sahlgrenska Academy and we will keep closely collaborating with researchers there. I will also retain an affiliation to the University of Gothenburg, at least for the near future.
All in all, this year will bring very interesting development, and this additional funding from the DDLS program will allow us to venture into new areas of bioinformatics and try out ideas that have previously been out of reach. I look forward to work with our new colleagues at Chalmers and within the DDLS program in the coming years!
A good-looking version of the Travel and Resistance paper
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]
Published paper: Travel spreads resistance genes
Earlier today, my most recent paper (1) became available online, describing resistance gene patterns in the gut microbiota of Swedes before and after travel to the Indian peninsula and central Africa. In this work, we have used metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs to show that the abundance of antibiotic resistance genes in several classes are increased after travel. This work reiterates the findings of several papers describing uptake of resistant bacteria (2-8) or resistance genes (9-11) after travel to destinations with worse resistance situation.
Our paper is important because it:
- Addresses the abundance of a vast range of resistance genes (more than 300).
- Finds evidence for that the overall relative abundance of antibiotic resistance genes increased after travel, without any intake of antibiotics.
- Shows that the sensitivity of metagenomics was, despite very deep sequencing efforts, not sufficient to detect acquisition of the low-abundant (CTX-M) resistance genes responsible for observed ESBL phenotypes.
- Reveals a “core resistome” of resistance genes that are more or less omnipresent, and remain relatively stable regardless of travel, while changes seem to occur in the more variable part of the resistome.
- Hints at increased abundance of Proteobacteria after travel, although this increase could not specifically be linked to resistance gene increases.
- Uses de novo metagenomic assembly to physically link resistance genes in the same sample, giving hints of co-resistance patterns in the gut microbiome.
The paper was a collaboration with Martin Angelin, Helena Palmgren and Anders Johansson at Umeå University, and was made possible by bioinformatics support from SciLifeLab in Stockholm. I highly recommend reading it as a complement to e.g. the Forslund et al. paper (12) describing country-specific antibiotic resistance patterns in the gut microbiota.
Taken together, this study offers a broadened perspective on how the antibiotic resistance potential of the human gut microbiome changes after travel, providing an independent complement to previous studies targeting a limited number of bacterial species or antibiotic resistance genes. Understanding how resistance genes travels the globe is hugely important, since resistance in principle only need to appear in a pathogen once; improper hygiene and travel may then spread novel resistance genes across continents rapidly (13,14).
- 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. Antimicrob Agents Chemother Accepted manuscript posted online (2015). doi: 10.1128/AAC.00933-15 [Paper link]
- Gaarslev K, Stenderup J: Changes during travel in the composition and antibiotic resistance pattern of the intestinal Enterobacteriaceae flora: results from a study of mecillinam prophylaxis against travellers’ diarrhoea. Curr Med Res Opin 9:384–387 (1985).
- Paltansing S, Vlot JA, Kraakman MEM, Mesman R, Bruijning ML, Bernards AT, Visser LG, Veldkamp KE: Extended-spectrum β-lactamase-producing enterobacteriaceae among travelers from the Netherlands. Emerging Infect. Dis. 19:1206–1213 (2013).
- Ruppé E, Armand-Lefèvre L, Estellat C, El-Mniai A, Boussadia Y, Consigny PH, Girard PM, Vittecoq D, Bouchaud O, Pialoux G, Esposito-Farèse M, Coignard B, Lucet JC, Andremont A, Matheron S: Acquisition of carbapenemase-producing Enterobacteriaceae by healthy travellers to India, France, February 2012 to March 2013. Euro Surveill. 19 (2014).
- Kennedy K, Collignon P: Colonisation with Escherichia coli resistant to “critically important” antibiotics: a high risk for international travellers. Eur J Clin Microbiol Infect Dis 29:1501–1506 (2010).
- Tham J, Odenholt I, Walder M, Brolund A, Ahl J, Melander E: Extended-spectrum beta-lactamase-producing Escherichia coli in patients with travellers’ diarrhoea. Scand. J. Infect. Dis. 42:275–280 (2010).
- Östholm-Balkhed Å, Tärnberg M, Nilsson M, Nilsson LE, Hanberger H, Hällgren A, Travel Study Group of Southeast Sweden: Travel-associated faecal colonization with ESBL-producing Enterobacteriaceae: incidence and risk factors. J Antimicrob Chemother 68:2144–2153 (2013).
- Kantele A, Lääveri T, Mero S, Vilkman K, Pakkanen SH, Ollgren J, Antikainen J, Kirveskari J: Antimicrobials increase travelers’ risk of colonization by extended-spectrum betalactamase-producing enterobacteriaceae. Clin Infect Dis 60:837–846 (2015).
- von Wintersdorff CJH, Penders J, Stobberingh EE, Oude Lashof AML, Hoebe CJPA, Savelkoul PHM, Wolffs PFG: High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerging Infect. Dis. 20:649–657 (2014).
- Tängdén T, Cars O, Melhus A, Löwdin E: Foreign travel is a major risk factor for colonization with Escherichia coli producing CTX-M-type extended-spectrum beta-lactamases: a prospective study with Swedish volunteers. Antimicrob Agents Chemother 54:3564–3568 (2010).
- Dhanji H, Patel R, Wall R, Doumith M, Patel B, Hope R, Livermore DM, Woodford N: Variation in the genetic environments of bla(CTX-M-15) in Escherichia coli from the faeces of travellers returning to the United Kingdom. J Antimicrob Chemother 66:1005–1012 (2011).
- Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P: Country-specific antibiotic use practices impact the human gut resistome. Genome Res 23:1163–1169 (2013).
- Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nat Rev Microbiol 13:396 (2015).
- Larsson DGJ: Antibiotics in the environment. Ups J Med Sci 119:108–112 (2014).
Metagenomics workshop at SciLifeLab
Science for Life Laboratories (SciLifeLab) in Stockholm will host a metagenome data analysis workshop on May 21-23, in which I will participate as a tutorial assistant. Additionally, our group leader Joakim Larsson will be giving a lecture about how we use metagenomics to assess the environmental reservoir of antibiotic resistance genes (much of my recent work will likely go into that). I hope to meet you there, so don’t forget to register!
Lex Nederbragt, Oslo University, Norway
Saskia Smits, Erasmus University Rotterdam, Netherlands
Joakim Larsson, Göteborg University, Sweden
Paul Wilmes, University of Luxembourg, Luxembourg
Anders Andersson, SciLifeLab, Sweden
Noan Le Bescot, UPMC (Tara expedition), France
The workshop is part of the AllBio Bioinformatics initiative.