Tag: Antibiotic resistance

Indian lake picked up by Indian media

It is nice to see that Indian media has picked up the story about antibiotic resistance genes in the heavily polluted Kazipally lake. In this case, it is the Deccan Chronicle who have been reporting on our findings and briefly interviewed Prof. Joakim Larsson about the study. The issue of pharmaceutical pollution of the environment in drug-producing countries is still rather under-reported and public perception of the problem might be rather low. Therefore, it makes me happy to see an Indian newspaper reporting on the issue. The scientific publication referred to can be found here.

A novel antibiotic? Pretty cool, but…

In a recent paper in Nature, a completely new antibiotic – teixobactin – is described (1). The really cool thing about this antibiotic is that it was discovered in a screen of uncultured bacteria, grown using new technology that enable controlled growth of single colonies in situ. I really like this idea, and I think the prospect of a novel antibiotic using a previously unexploited mechanism is super-promising, particularly in the light of alarming resistance development in clinically important pathogens (2,3). What really annoys me about the paper is the claim (already in the abstract) that since “we did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin (…) the properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.” To me, this sounds pretty much like a bogus statement; in essence telling me that we apparently have not learned anything from the 70 years of antibiotics usage and resistance development. After working with antibiotic resistance a couple of years, particularly from the environmental perspective, I have a very disturbing feeling that there is already resistance mechanisms against teixobactin waiting out in the wild (4,5). Pretending that lack of mutation-associated resistance development means that there could not be resistance development did not help vancomycin (6,7), and we now see VRE (Vancomycin Resistant Enterococcus) showing up as a major problem in clinics. The “avoid development of resistance” claim is downright irresponsible, and the cynic in me cannot help to think that NovoBiotic Pharmaceuticals (the affiliation of almost half of the authors) has a monetary finger in this jar. In the end, time will tell how “resistance-resilient” teixobactin is and how well we can handle the gift of a novel antibiotic.

  1. Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K: A new antibiotic kills pathogens without detectable resistance. Nature (2015). doi:10.1038/nature14098
  2. Finley RL, Collignon P, Larsson DGJ, McEwen SA, Li X-Z, Gaze WH, Reid-Smith R, Timinouni M, Graham DW, Topp E: The scourge of antibiotic resistance: the important role of the environment. Clin Infect Dis, 57: 704–710 (2013).
  3. French GL: The continuing crisis in antibiotic resistance. Int J Antimicrob Agents, 36 Suppl 3:S3–7 (2010).
  4. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5: 648 (2014).
  5. Larsson DGJ: Antibiotics in the environment. Ups J Med Sci, 119: 108–112 (2014).
  6. Wright GD: Mechanisms of resistance to antibiotics. Curr Opin Chem Biol, 7:563–569 (2003).
  7. Werner G, Strommenger B, Witte W: Acquired vancomycin resistance in clinically relevant pathogens. Future Microbiol, 3: 547–562 (2008).

Looking for a super-interesting job in bioinformatics?

If you’re looking for super-interesting jobs within bioinformatics, you don’t need to look any further. Instead, you should apply for a position at 1928 Diagnostics here in Gothenburg and join them in the fight against antibiotic resistant bacteria. The position is in the development team and the deadline for application is December 19. All the details can be found here.

Polluted lake paper in final form

Our paper describing the bacterial community of a polluted lake in India has now been typeset and appears in its final form in Frontiers in Microbiology. If I may say so, I think that the paper turned out to be very goodlooking and it is indeed nice to finally see it in print. The paper describes an unprecedented diversity and abundance of antibiotic resistance genes and genes enabling transfer of DNA between bacteria. We also describe a range of potential novel plasmids from the lake. Finally, the paper briefly describes a new approach to targeted assembly of metagenomic data — TriMetAss — which can be downloaded here.

Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648

TriMetAss – A Trinity-based targeted metagenomics assembler

With the publication of my latest paper last week (1), I also would like to highlight some of the software underpinning the findings a bit. To get around the problem that extremely common resistance genes could be present in multiple contexts and variants, causing assembler such as Velvet (2) to perform sub-optimally, we have written a software tool that utilizes Vmatch (3) and Trinity (4) to iteratively construct contigs from reads associated with resistance genes. This could of course be used in many other situations as well, when you want to specifically assemble a certain portion of a metagenome, but suspect that that portion might be found in multiple contexts.

TriMetAss is a Perl program, employing Vmatch and Trinity to construct multi-context contigs. TriMetAss uses extracted reads associated with, e.g., resistance genes as seeds for a Vmatch search against the complete set of read pairs, extracting reads matching with at least 49 bp (by default) to any of the seed reads. These reads are then assembled using Trinity. The resulting contigs are then used as seeds for another search using Vmatch to the complete set of reads, as above. All matches (including the previously matching read pairs) are again then used for a Trinity assembly. This iterative process is repeated until a stop criteria is met, e.g. when the total number of assembled nucleotides starts to drop rather than increase. The software can be downloaded here.


  1. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648
  2. Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821–829 (2008). doi:10.1101/gr.074492.107
  3. Kurtz S: The Vmatch large scale sequence analysis software (2010). http://vmatch.de/
  4. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al.: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29, 644–652 (2011). doi:10.1038/nbt.1883

Published paper: Antibiotic resistance genes in a polluted lake

The first work in which I have employed metagenomics to investigate antibiotic resistance has been accepted in Frontiers in Microbiology, and is (at the time of writing) available as a provisional PDF. In the paper (1), which is co-authored by Fredrik Boulund, Jerker Fick, Erik Kristiansson and Joakim Larsson, we have used shotgun metagenomic sequencing of an Indian lake polluted by dumping of waste from pharmaceutical production. We used this data to describe the diversity of antibiotic resistance genes and the genetic context of those, to try to predict their genetic transferability. We found resistance genes against essentially every major class of antibiotics, as well as large abundances of genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant in the polluted lake than in a Swedish lake included for comparison, where only eight resistance genes were found. The abundances of resistance genes have previously only been matched by river sediment subject to pollution from pharmaceutical production (2). In addition, we describe twenty-six known and twenty-one putative novel plasmids from the Indian lake metagenome, indicating that there is a large potential for horizontal gene transfer through conjugation. Based on the wide range and high abundance of known resistance factors detected, we believe that it is plausible that novel resistance genes are also present in the lake. We conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes. This work further highlights previous findings that pharmaceutical production settings could provide sufficient selection pressure from antibiotics (3) to drive the development of multi-resistant bacteria (4,5), resistance which may ultimately end up in pathogenic species (6,7). The paper can be read in its entirety here.


  1. Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, Volume 5, Issue 648 (2014). doi: 10.3389/fmicb.2014.00648
  2. Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, Söderström H, Larsson DGJ: Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE, Volume 6, e17038 (2011). doi:10.1371/journal.pone.0017038.
  3. Larsson DGJ, de Pedro C, Paxeus N: Effluent from drug manufactures contains extremely high levels of pharmaceuticals. J Hazard Mater, Volume 148, 751–755 (2007). doi:10.1016/j.jhazmat.2007.07.008
  4. Marathe NP, Regina VR, Walujkar SA, Charan SS, Moore ERB, Larsson DGJ, Shouche YS: A Treatment Plant Receiving Waste Water from Multiple Bulk Drug Manufacturers Is a Reservoir for Highly Multi-Drug Resistant Integron-Bearing Bacteria. PLoS ONE, Volume 8, e77310 (2013). doi:10.1371/journal.pone.0077310
  5. Johnning A, Moore ERB, Svensson-Stadler L, Shouche YS, Larsson DGJ, Kristiansson E: Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production. Appl Environ Microbiol, Volume 79, 7256–7263 (2013). doi:10.1128/AEM.02141-13
  6. Pruden A, Larsson DGJ, Amézquita A, Collignon P, Brandt KK, Graham DW, Lazorchak JM, Suzuki S, Silley P, Snape JR., et al.: Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environ Health Perspect, Volume 121, 878–885 (2013). doi:10.1289/ehp.1206446
  7. Finley RL, Collignon P, Larsson DGJ, McEwen SA, Li X-Z, Gaze WH, Reid-Smith R, Timinouni M, Graham DW, Topp E: The scourge of antibiotic resistance: the important role of the environment. Clin Infect Dis, Volume 57, 704–710 (2013). doi:10.1093/cid/cit355

PhD position: Come and work with us!

If you are thinking about doing a PhD and think that bioinformatics and antibiotic resistance is a cool subject, then now is your chance to come and join us for the next four years! There is a PhD position open i Joakim Larsson’s group, which means that if you get the job you will work with me, Joakim Larsson, Erik Kristiansson, Ørjan Samuelsen and Carl-Fredrik Flach on a super-interesting project relating to discovery of novel beta-lactamase genes (NoCURE). The project aims to better understand where, how and under what circumstances these genetic transfer events take place, in order to provide opportunities to limit or delay resistance development and thus increase the functional lifespan of precious antibiotics. The lion’s share of the work will be related to interpreting large-scale sequencing data generated by collaborators within the project; both genome sequencing and metagenomic data.

This is a great opportunity to prove your bioinformatics skills and use them for something urgently important. Full details about the position can be found here.

PhD position with Erik Kristiansson

If you’re looking for a PhD position in bioinformatics, working with antibiotic resistance, there’s an opening in Erik Krisiansson’s (best bioinformatician in Gothenburg? I think so) group. To apply you need to have a master’s level degree in bioinformatics, mathematical statistics, mathematics, computer science, physics, molecular biology or any equivalent topic, obtained latest June 2014. If you’re a master student and want to join us, this is your chance! You can read more and apply for the position here.

New year – Some updates

A new year has begun, and it brings with it a few updates on the website. I have added a summary of the year 2013 from my perspective, and (as you may recognize) updated my picture on the front page. Briefly, this year will bring lots of exciting stuff. Personally, I am quite excited to finally be able to share the new version of Metaxa – Metaxa2 – which will be released to the public late this Winter (or early Spring). Additionally, I look forward to wrap up some manuscript on metagenomics and antibiotic resistance, which I have been working with for more than 2.5 years now. Also, we look forward to some super-intersting technology developments in DNA sequencing, with PacBio finally finding proper usage scenarios, Nano-pore sequencing around the corner, and super-multiplexing on the Illumina instruments. We’re in for a treat with DNA sequencing in 2014!

Published paper: BacMet Database

It seems like our paper on the recently launched database on resistance genes against antibacterial biocides and metals (BacMet) has gone online as an advance access paper in Nucleic Acids Research today. Chandan Pal – the first author of the paper, and one of my close colleagues as well as my roommate at work – has made a tremendous job taking the database from a list of genes and references, to a full-fledged browsable and searchable database with a really nice interface. I have contributed along the process, and wrote the lion’s share of the code for the BacMet-Scan tool that can be downloaded along with the database files.

BacMet is a curated source of bacterial resistance genes against antibacterial biocides and metals. All gene entries included have at least one experimentally confirmed resistance gene with references in scientific literature. However, we have also made a homology-based prediction of genes that are likely to share the same resistance function (the BacMet predicted dataset). We believe that the BacMet database will make it possible to better understand co- and cross-resistance of biocides and metals to antibiotics within bacterial genomes and in complex microbial communities from different environments.

The database can be easily accessed here: http://bacmet.biomedicine.gu.se, and use of the database in scientific work can cite the following paper, which recently appeared in Nucleic Acids Research:

Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DGJ: BacMet: Antibacterial Biocide and Metal Resistance Genes Database. Nucleic Acids Research. Database issue, advance access. doi: 10.1093/nar/gkt1252 [Paper link]