Microbiology, Metagenomics and Bioinformatics

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

Browsing Posts tagged EDAR2015

I have had the pleasure to be chosen as a speaker for next week’s (ten days from now) Swedish Bioinformatics Workshop. My talk is entitled “Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data“, and will largely deal with the same questions as my talk on EDAR3 in May this year. As then, the talk will highlight the some particular pitfalls related to interpretation of data, and exemplify how flawed analysis practices can result in misleading conclusions regarding community function, and use examples from our studies of environments subjected to pharmaceutical pollution in India, the effect of travel on the human resistome, and modern municipal wastewater treatment processes.

The talk will take place on Thursday, September 24, 2015 at 16:30. The full program for the conference can be found here. And also, if you want a sneak peak of the talk, you can drop by on Friday 13.00 at Chemistry and Molecular Biology, where I will give a seminar on the same topic in the Monthly Bioinformatic Practical Meetings series.

Late last year, an opinion paper by José Martínez, Teresa Coque and Fernando Baquero was published in Nature Reviews Microbiology (1). In this paper, the authors present a system – resistance readiness conditions (RESCon) – for ranking the risks associated with the detection of antibiotic resistance genes. They also outline the obstacles associated with determining risks presented by antibiotic resistance genes in environmental microbial communities in terms of their potential to transfer to human pathogens. Generally, I am very positive about this paper, which I think is a must-read for anyone who works with antibiotic resistance genes in metagenomes, regardless of it they stem from the human gut or the external environment.

There is, however, one very important aspect that struck me and many other members of our research group as curious: the proposed system assign antibiotic resistance genes already present on mobile genetic elements in human pathogens to the highest risk category (RESCon 1), while resistance genes encoding novel resistance mechanisms not yet been found on mobile elements in a pathogen are considered to be part of lower risk categories. We believe that this system will overestimate the risks associated with well-known resistance factors that are already circulating among human pathogens and under-appreciate the potentially disastrous consequences that the transfer of previously unknown resistance determinants from the environmental resistome could have (exemplified by the rapid clinical spread of the NDM-1 metallo-beta-lactamase gene (2,3)).

With this in mind me and Joakim Larsson wrote a response letter to Nature Reviews Microbiology that went online last monday (4), together with the authors’ reply to us (5). (I strongly suggest that you read the entire original paper (1) before you read the reply (5) to our response letter (4), since Martinez et al. changes the scope slightly from the original paper in their response letter, and these clarifications may (or may not) have been in response to our arguments.)

In our response, we also stress that the abundances of resistance genes, and not only their presence, should be accounted for when estimating risks (although that last point might have been slightly obscured due to the very low word limit). In other words, we think that identifying environmental hotspots for antibiotic resistance genes, where novel resistance genes could be selected for (6,7,8), is of great importance for mitigating public health risks related to environmental antibiotic resistance. Please read our full thoughts on the matter in Nature Reviews Microbiology.

Similar issues will be touched upon in my talk at the EDAR2015 conference later in May. Hope to see you there!

References

  1. Martinez JL, Coque TM, Baquero F: What is a resistance gene? Ranking risk in resistomes. Nat Rev Microbiol 2015, 13:116–123.
  2. Kumarasamy KK, et al.: Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis 2010, 10:597–602.
  3. Walsh TR, Weeks J, Livermore DM, Toleman MA: Dissemination of NDM‐1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis 2011, 11:355–362.
  4. Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nat Rev Microbiol 2015, Advance online publication. doi:10.1038/nrmicro3399‐c1
  5. Martinez JL, Coque TM, Baquero F: Prioritizing risks of antibiotic resistance genes in all metagenomes. Nat Rev Microbiol 2015, Advance online publication. doi:10.1038/nrmicro3399‐c2
  6. Kristiansson E, et al.: Pyrosequencing of antibiotic‐contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE 2011, 6:e17038.
  7. 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. Front Microbiol 2014, 5:648.
  8. Marathe NP, et al.: A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi‐drug resistant integron‐bearing bacteria. PLoS ONE 2013, 8:e77310.

I will be giving a talk at the Third International symposium on the environmental dimension of antibiotic resistance (EDAR2015) next month (five weeks from now. The talk is entitled “Turn up the signal – wipe out the noise: Gaining insights into antibiotic resistance of bacterial communities using metagenomic data“, and will deal with handling of metagenomic data in antibiotic resistance gene research. The talk will highlight the some particular pitfalls related to interpretation of data, and exemplify how flawed analysis practices can result in misleading conclusions regarding antibiotic resistance risks. I will particularly address how taxonomic composition influences the frequencies of resistance genes, the importance of knowledge of the functions of the genes in the databases used, and how normalization strategies influence the results. Furthermore, we will show how the context of resistance genes can allow inference of their potential to spread to human pathogens from environmental or commensal bacteria. All these aspects will be exemplified by data from our studies of environments subjected to pharmaceutical pollution in India, the effect of travel on the human resistome, and modern municipal wastewater treatment processes.

The talk will take place on Monday, May 18, 2015 at 13:20. The full scientific program for the conference can be found here. Registration for the conference is still possible, although not for the early-bird price. I look forward to see a lot of the people who will attend the conference, and hopefully also you!