Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

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My name is Johan Bengtsson-Palme. I am an assistant professor at the Sahlgrenska Academy, residing in Gothenburg on the Swedish west coast. My research concerns microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance and interactions in bacterial communities through metagenomics and bioinformatics. I also have an interest in molecular taxonomy and improving the quality of reference databases. I work closely with the group of Joakim Larsson, Erik Kristiansson and Henrik Nilsson. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se

BMC Genomics today published a paper first-authored by my long-time colleague Fredrik Boulund, which describes a computational screen of genomes and metagenomes for novel qnr fluoroquinolone resistance genes (1). The study makes use of Fredrik’s well-designed and updated qnr-prediction pipeline, but in contrast to his previous publication based on the pipeline from 2012 (2), we here study a 20-fold larger dataset of almost 13 terabases of sequence data. Based on this data, the pipeline predicted 611 putative qnr genes, including all previously described plasmid-mediated qnr gene families. 20 of the predicted genes were previously undescribed, and of these nine were selected for experimental validation. Six of those tested genes improved the survivability under ciprofloxacin exposure when expressed in Escherichia coli. The study shows that qnr genes are almost ubiquitous in environmental microbial communities. This study also lends further credibility to the hypothesis that environmental bacterial communities can act as sources of previously uncharacterized antibiotic resistance genes (3-7). The study can be read in its entirety here.

References

  1. Boulund F, Berglund F, Flach C-F, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E: Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics, 18, 682 (2017). doi: 10.1186/s12864-017-4064-0
  2. Boulund F, Johnning A, Pereira MB, Larsson DGJ, Kristiansson E: A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences. BMC Genomics, 13, 695 (2012). doi: 10.1186/1471-2164-13-695
  3. Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nature Reviews Microbiology, 13, 369 (2015). doi: 10.1038/nrmicro3399-c1
  4. Allen HK, Donato J, Wang HH et al.: Call of the wild: antibiotic resistance genes in natural environments. Nature Reviews Microbiology, 8, 251–259 (2010).
  5. Berendonk TU, Manaia CM, Merlin C et al.: Tackling antibiotic resistance: the environmental framework. Nature Reviews Microbiology, 13, 310–317 (2015).
  6. Martinez JL: Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens. Frontiers in Microbiology, 2, 265 (2011).
  7. Finley RL, Collignon P, Larsson DGJ et al.: The scourge of antibiotic resistance: the important role of the environment. Clinical Infectious Diseases, 57, 704–710 (2013).

I just wanted to notify anyone who might be interested in following my more personal reflections on my month in Wisconsin (and in Michigan over EDAR4) that I will be updating my Wisconsin Blog at this site (hopefully) regularly. The blog updates are not visible on the first page, so you will have to actively go to the Wisconsin Blog page by clicking in the upper right of the page.