Summary of 2019

This year started as we had just returned for a quite overwhelming year in the United States. I spent the first couple of months of the year on parental leave with my one-year-old and in July I started my four-year contract with the University of Gothenburg, with full funding for my salary as well as a big bag of extra money, most of which will go to cover the salary of a PhD student.

In June, I was awarded the very first Lennart Sparell prize from Cancer- och Allergifonden [the Swedish Cancer and Allergy fund]. The prize was instated in memory of the foundations founder – Lennart Sparell, who passed away in 2018 – and was awarded to because of my research on the role of ecological and evolutionary processes in the external environment in driving antibiotic resistance development, how that can have consequences for human health, and how this has pushed the paradigm boundaries of the field. I am greatly honoured by this prize and will make sure to use the prize money wisely!

Over the summer, Alice Zublena visited the lab and did an excellent project on the effects of different beta-lactam antibiotic on the members of the THOR community, and in August and September, Adriana Osińska visited the lab to work on analysis of InSeq data. In September, Emil Burman joined the lab as a master student, working on invasion in the THOR model community.

From a publication point of view, it was a calm year. My biggest two publications were one describing the microbiome and resistome of a Croatian treatment plant that receives wastewater from macrolide antibiotic production, together with Nikolina Udiković Kolić, and another describing our software package Mumame, on which Shruthi Magesh (now a PhD student in the Handelsman lab) was first author. I was also involved in a paper on diarrheal bacterial pathogens and multi-resistant enterobacteria in a Bolivian river and an opinion paper on next-generation sequencing and antimicrobial resistance. I also wrote a book chapter with Stefanie Heß on strategies to reduce or eliminate resistant pathogens in the environment, which was published late in the year.

In June, I was recruited to an EFSA expert group working with antibiotic concentration limits in animal feed, which allowed me to take three trips to Parma in Italy. I also traveled to The Netherlands in the spring for the ICOHAR conference, to talk about antibiotic resistance in a one-health perspective. In June, I got to visit San Francisco for the first time, when I attended ASM Microbe and gave a talk on antibiotic resistance and how it relates to my work in the Handelsman lab.

In November, our application to JPIAMR for the EMBARK program got funding, which means that during 2020 to 2022 I will be developing a better framework for environmental monitoring of antibiotic resistance together with an incredible team of scientists! I also received a Sahlgrenska Academy International Starting Grant of 1 million SEK, which I am incredibly thankful for and which will greatly enhance what we can do in the coming years. I look forward to start spending all these research money and recruiting more people to the lab in 2020!

Publications

Papers

Brown P, RELISH Consortium, Zhou Y: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database, 2019: 1–66 (2019). doi: 10.1093/database/baz085 [Paper link]
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 [Paper link]
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 [Paper link]
Guzman-Otazo J, Gonzales-Siles L, Poma V, Bengtsson-Palme J, Thorell K, Flach C-F, Iñiguez V, Sjöling Å: Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia. PLoS ONE, 14, 1, e0210735 (2019). doi: 10.1371/journal.pone.0210735[Paper link]
Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K: The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47, D1, D259–D264 (2019). doi: 10.1093/nar/gky1022 [Paper link] (Published in 2018, but noted as a 2019 paper)
Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH: Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources, 19, 1, 118–127 (2019). doi: 10.1111/1755-0998.12944 [Paper link] (Published in 2018, but noted as a 2019 paper)

Book chapters and opinion papers

Ruppé E, Bengtsson-Palme J, Charretier Y, Schrenzel J: How next-generation sequencing can address the antimicrobial resistance challenge. AMR Control, 2019-20, 60-65 (2019). [Paper link]
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]
Bengtsson-Palme J: Assessment and management of risks associated with antibiotic resistance in the environment. In: Roig B, Weiss K, Thoreau V (Eds.) Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment, 243–263. Elsevier, UK (2019). doi: 10.1016/B978-0-12-813290-6.00010-X [Paper link] (Published in 2018, but noted as a 2019 book)

Conference talks

Bengtsson-Palme J: The Effect of Antibiotics on Interactions in Microbial Communities ASM Microbe 2019, San Francisco, CA, USA, 2019.
Bengtsson-Palme J: The environment and antibiotic resistance development – now and in the future ICOHAR 2019, Utrecht, Netherlands, 2019.

Posters

Bengtsson-Palme J, Garavito MF, Osińska A, Hurley A, Rajendhran J, Burman E, Kristiansson E, Lozano GL, Handelsman J: Large-scale identification of genes important for bacterial community invasion. Swedish Bioinformatics Workshop, Göteborg, Sweden, 2019.

Conferences and workshops

ICOHAR 2019
in Utrecht, The Netherlands (invited talk)
ASM Microbe 2019
in San Francisco, CA, USA (invited talk)
Swedish Bioinformatics Workshop
in Göteborg, Sweden (poster and workshop)

Research platforms and projects

CARe
Centre for Antibiotic Resistance Research at University of Gothenburg
UNITE
The database for DNA identification of fungi
GOTBIN – Gothenburg Bioinformatics Network

Other committees etc.

Member of the expert panel for refinement of the criteria used for procurement of medicines in Sweden
Member of the JRC external expert group for implementation of NGS in the coordinated action plan against antimicrobial resistance
Member of the expert panel for development of antibiotic concentration limits in animal feed, organized by the European Food Safety Authority (EFSA)
Member of the SBW2019 Organizing Committee
Member of the GOTBIN working group
Reviewed manuscripts for Methods in Ecology & Evolution, Bioinformatics, Science of the Total Environment, Environmental Science & Technology, Journal of Environmental Quality, Journal of Cleaner Production, Nature Springer Books, Nature Communications, Ecology Letters, Journal of Global Antimicrobial Resistance, Trends in Microbiology, Environmental Pollution, FEMS Microbiology Ecology, Science Advances, Microbiome, Journal of Hazardous Materials, Chemical Engineering Journal, Environment International, Environmental Science and Pollution Research, and Genome Biology
Reviewed grant applications for The Natural Sciences and Engineering Research Council of Canada (NSERC), Italian Ministry of Education, University and Research (MIUR), US National Science Foundation (NSF), Institut Pasteur, and University of Piemonte Orientale