Published paper: Computational discovery of novel qnr genes

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).

Students are coming back

Surface tension on 96-well plate
Surface tension - or what we have been working with over the last few days
I’ve spend the lion’s share of the past few days in the lab, working quite late to obtain supercool results that we will now verify over the weekend. It’s very exciting to be able to generate useful data already during your first week in the lab (after not doing wet lab work for years), but mostly this is thanks to Manuel. Anyway, look at the beauty of those plates! My new favorite color must be crystal violet.

Students are back
Students are back, and with that 'all campus worship', whatever that is
Another thing that has happened over the past week is that the students are beginning to come back her for the autumn semester. This means nice little paintings on the ground, lots of things happening downtown, but also that it’s harder to sleep since the previously quiet area of college dorms is not seeing quite a significant amount of nightlife. Large packs of students passing by my window at night, talking loudly. It’s mostly nice though. There are many parallels between Uppsala and Madison – both are cities heavily centered around their universities, and both seem to die a little during summers when the students move out. The differences mainly are that Madison is much more beautifully located between three lakes, that Uppsala has a much older history, and that Madison seems to have quite a bit of nightlife also in the summertime.

Almost there
Almost there...
On Monday I will go to see a house to rent next year. Please keep your fingers crossed that it’s good and, if so, that we’ll get it! Otherwise housing has been a bit of a hassle, since everyone wants to rent now before the autumn semester. But I hope that that problem will no longer be a problem on Monday. Have a nice weekend!

On my way to work
On my way to work

Manuel, my hero

Okay, first of all this is a shoutout post to Manuel Garavito, who has been putting up with me for the last two days – my first two days in a wet lab for several years. Manuel has been beyond fantastic in showing me their basic protocols and having patience with my rusty lab skills. If this project will work out, it will very much be because of him.

The Hop CatThis weekend, there haven’t been a lot of time for other things than lab work, but I spent Friday evening at the Memorial Union where I happened to stumble into a concert with Brazilian (I think, not sure) music. And on Saturday evening I went out to the Hop Cat, where I tasted the fantastic beer Psychedellic Cat Grass and got taught the basics of American football by a woman who was also there on her own, apparently to watch the game. So, I’m doing my well but working my ass off with things I am not really that good at. Yet.

Back in Madison

Eagle Heights
Eagle Heights
Hey, sorry for disappearing for more than a week. The EDAR conference (more on that in a later post) was super-intense and the weekend with my Gothenburg research group in Munising in northern Michigan was fantastic but didn’t really leave any time for writing. And after that I have been quite messed up emotionally, feeling very lonely and started doubting my project and … well everything. But it’s looking better now again. Yesterday evening I was out dancing lindy hop at The Brink. Although I only did a few dances, it was very nice to do something that was all about feeling good and playing, and not so serious.

Shorewood Hills
Shorewood Hills
Today I have instead spent my evening doing grocery shopping at Whole Foods (what a fantastic store that is!) and checking out the areas where the University of Wisconsin keep their university housing. Oh, how I wish that we could get somewhere to live there. The surroundings are absolutely beautiful and there were kids everywhere on the lawns. That said, the queues for staying there are most likely very long. By the way, if anyone would have an insider tip on where and how to find good places to live in Madison, all input is appreciated. Tonight, Madison has been good to me.

Frautschi Point
Frautschi Point

Madison is beautiful

Memorial Union, Madison
Memorial Union, Madison

Today I spent some time walking in the other direction from the University. Gabriel suggested I took the walk by Lake Mendota downtown, and that was a really nice walk through the forest, just by the lake. After dinner, I had ice cream on one of the landings on the picture. Madison is really a nice and beautiful city; I look forward to going here with my family next year.

Tomorrow, I am in for a six hours drive to Lansing and the EDAR conference. I hope to be writing a little about my thoughts on the conference as well, but we’ll see if I will have time to get around to that…

The Wisconsin Blog

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.

My first day in Madison

Wisconsin Institute of Discovery
Wisconsin Institute of Discovery
So, I have arrived in Madison, WI. I had a 17 hour flight yesterday, and I am quite messed-up with my perception of time, but except for that i’m good. I spend the morning walking around in Madison (and found a really nice coffee place – Colectivo) and getting a phone contract. Madison really is a very beautiful and green town, which reminds me quite a lot of an “American Uppsala”. After that, I had lunch with the majority of the Jo Handelsman lab at the Wisconsin Institute of Discovery Building, and then Manuel spent the afternoon showing me the experimental system we’re going to use (and its quirks). Lots and lots of new things to take in and choices to consider. This will be an interesting year. Now, I will try to find a place to eat and get a beer before I’m too tired (it’s half past one in the morning in Sweden as I’m writing this…) I look forward to my coming month here, but I also miss my family a lot already.
Lake Mendota
Lake Mendota

Published paper: The Calanus glacialis mitogenome

Mitochondrial DNA Part B today published a mitochondrial genome announcement paper (1) in which I was involved in doing the assemblies and annotating them. The paper describes the mitogenome of Calanus glacialis, a marine planktonic copepod, which is a keystone species in the Arctic Ocean. The mitogenome is 20,674 bp long, and includes 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. While this is of course note a huge paper, we believe that this new resource will be of interest in understanding the structure and dynamics of C. glacialis populations. The main work in this paper has been carried out by Marvin Choquet at Nord University in Bodø, Norway. So hats off to him for great work, thanks Marvin! The paper can be read here.

Reference

  1. Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G: The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2, 2, 506–507 (2017). doi: 10.1080/23802359.2017.1361357 [Paper link]

New employment – same work

Today, I started my new position at the University of Gothenburg as a non-tenured assistant professor (forskarassistent)*. In essence, this means that I have a position funded by my own grant until the end of 2020, although I will be on a leave-of-absence while doing my PostDoc with Jo Handelsman in Wisconsin. Speaking of which, I will be leaving to the US on Thursday next week for a month of setting things up at her lab (and also going to the EDAR4 conference in Lansing). I will return to Sweden in mid-September and leave for the US for real early next year.

In terms of actual work, this change of position will not mean very much at the moment. I will continue to do the same things for some time, and I will remain closely associated with Joakim Larsson’s lab at the Dept. of Infectious Diseases. And luckily, I will retain my lovely roommates for at least the time being. In the long run, however, this means that I will shift my research focus slightly, away from antibiotic resistance risk management towards interactions in microbial communities (still related to antibiotics though). Exciting times ahead!

Note
* For some reason, the university administration refuses to call this position assistant professor in English at this time, instead referring to the position as “Postdoctoral research fellow”. I guess that it might be bloody annoying explaining that this is not the same as “postdoctoral researcher” and virtually everywhere else would be called “(non-tenured) assistant professor”, but then on the other hand, who cares about titles anyway?

Published paper: Helicobacter pylori vs. the viable gastric microbiota

I have just returned from a week of vacation in Sicily (almost without internet access), so I am a tad late to this news, but earlier this week Infection and Immunity published our paper on the Helicobacter pylori transcriptome in gastric infection (and early stages of carcinogenesis), and how that relates to the transcriptionally active microbiota in the stomach environment (1). This paper has been long in the making (an earlier version of it was included in Kaisa Thorell’s PhD thesis (2)), but some late additional analyses did substantially strengthen our confidence in the suggestions we got from the original data.

In the paper (1) we use metatranscriptomic RNAseq to investigate the composition of the viable microbial community, and at the same time study H. pylori gene expression in stomach biopsies. The biopsies were sampled from individuals with different degrees of H. pylori infection and/or pre-malignant tissue changes. We found that H. pylori completely dominates the microbiota in infected individuals, but (somewhat surprisingly) also in the majority of individuals classified as H. pylori uninfected using traditional methods. This confirms previous reports that have detected minute quantities of H. pylori also in presumably uninfected individuals (3-6), and raises the question of how large part of the human population (if any) that is truly not infected/colonized by H. pylori. The abundance of H. pylori was correlated with the abundance of Campylobacter, Deinococcus, and Sulfurospirillum. It is unclear, however, if these genera only share the same habitat preferences as Helicobacter, or if they are specifically promoted by the presence of H. pylori (or tissue changes induced by it). We also found that genes involved in pH regulation and nickel transport were highly expressed in H. pylori, regardless of disease stage. As far as we know, this study is the first to use metatranscriptomics to study the viable microbiota of the human stomach, and we think that this is a promising approach for future studies on pathogen-microbiota interactions. The paper (in unedited format) can be read here.

References

  1. Thorell K, Bengtsson-Palme J, Liu OH, Gonzales RVP, Nookaew I, Rabeneck L, Paszat L, Graham DY, Nielsen J, Lundin SB, Sjöling Å: In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis. Infection and Immunity, accepted manuscript (2017). doi: 10.1128/IAI.00031-17 [Paper link]
  2. Thorell K: Multi-level characterization of host and pathogen in Helicobacter pylori-associated gastric carcinogenesis. Doctoral thesis, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg (2014). [Link]
  3. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Reman DA: Molecular analysis of the bacterial microbiota in the human stomach. PNAS, 103:732-737 (2006).
  4. Dicksved J, Lindberg M, Rosenquist M, Enroth H, Jansson JK, Engstrand L: Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls. Journal of Medical Microbiology, 58:509-516 (2009).
  5. Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG: Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME Journal, 5:574-579 (2011).
  6. Li TH, Qin Y, Sham PC, Lau KS, Chu KM, Leung WK: Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis. Scientific Reports, 7:44935 (2017).