Tag: Environment

More on antibiotic resistance genes as pollutants

I received some well-formulated and very much relevant critique on my post Why viewing antibiotic resistance genes as a pollutant is a problem, which I wrote in January. To encourage the debate on this issue, I have asked the author – Amy Pruden – for her permission to republish it here, to give it the visibility it deserves. I intend to follow up on her comments in a forthcoming post, but I have not had time to formulate my answer yet. Until then, please read and contemplate both the original post by me, and Amy’s highly relevant answer below. I hope that we can continue this discussion in the same fruitful manner!

First of all I thank Johan Bengtsson for initiating a lively and much needed discussion on which pollutant we should precisely be targeting, antibiotics or antibiotic resistance genes (ARGs), in our important war against the spread of antibiotic resistance. As Bengtsson correctly alludes, my perspective comes from that of environmental science and engineering. At the core of these disciplines is defining and predicting the fate of pollutants in the environment, as well as designing appropriate means for their control. For these purposes, the definition of the pollutant of interest is of central importance. In general they may be defined as “undesired or harmful constituents within an environmental matrix, usually of human origin.” Pollutants may be classified in all shapes and sizes, including conservative (i.e., not subject to degradation or growth), non-conservative, biotic, abiotic, dissolved, and suspended (i.e., not dissolved). Thus, the first point, regarding the nature by which ARGs are spread disqualifying them from being considered as pollutants, is inaccurate.

At the same time, I recognize and agree that ARGs are indeed a natural and important aspect of the natural ecosystem. I commend recent work revealing the vast “antibiotic-resistome” in ancient environments (D’Costa et al. 2011; Allen et al. 2009), as it provides an essential understanding of the baseline antibiotic resistance in the pre-antibiotic era, which may serve as contrast for observations in the current antibiotic era. Thus, I agree that not all ARGs are pollutants, rather, anthropogenic sources of ARGs are the agents of interest. Perhaps I and others are guilty of not making this distinction more clear. It should also be pointed out that likewise, the vast majority of antibiotics in use today are derived from natural compounds, yet I agree that they can also serve as important environmental pollutants of concern. Thus, it is not necessarily whether the constituent is naturally occurring that defines the pollutant, rather its magnitude and distribution, as influenced by human activities.

It is agreed that viewing ARGs as contaminants does pose technical challenges. They may amplify within a host, or attenuate due to degradation or diminished selection pressure. However, with appropriate understanding of the mechanisms of transport and persistence, accurate models may be developed. I do contend that the jury is still out regarding the relative importance of extracellular and intracellular ARGs. The pool of extracellular DNA remains vastly uncharacterized, and some studies suggest that it is more extensive than previously thought (Wu et al. 2009; Corinaldesi et al. 2005). Other studies have specifically demonstrated the capability of extracellular ARGs to persist under certain environmental conditions and maintain its integrity for host uptake (Cai et al. 2007). While focusing attention on individual resistant strains of bacteria has merit in some instances, this approach is also greatly limited by the unculturability of the vast majority of environmental microbes. As we have now entered the metagenomic era, we now have the tools to tackle the complexity of resistance elements in the environment and precisely define the human influence. Distribution of ARGs may also be considered in parallel with key genetic elements driving their horizontal gene transfer, such as plasmids, transposons, and integrons.

Regarding the antibiotics themselves, clearly they are important. The direct relationship between clinical use and increasing rates of antibiotic resistance is well-documented and certainly continued vigilance in promoting their appropriate use and disposal is called for. What remains much foggier is the exact role of environmental antibiotics in enabling selection once released into the environment. There is good evidence that even sub-inhibitory levels of antibiotics can stimulate various functions in the cell, especially horizontal gene transfer, as reviewed recently by Aminov (2011). However, environmentally-relevant concentrations driving selection of resistant strains are largely unknown. Further, at what point along a discharge pathway from wastewater treatment plant or livestock lagoon do ARGs persist independently of ambient antibiotic conditions? Indeed, some studies have noted correlations between antibiotics and ARGs in environmental matrices while others have noted an absence of such a correlation. In either case, it appears that ARGs persist and are transported further along pathways than antibiotics, suggesting distinct factors governing transport (McKinney et al. 2010; Peak et al. 2007). Research is needed to better understand the mechanisms at play, such as antibiotics other selectors (e.g. metals and other toxins), in leaving a human foot-print on environmental reservoirs of resistance. Nonetheless, a reasonable approach for mitigating risk seems to be focusing attention on developing appropriate technologies for eliminating both antibiotics and genetic material from wastestreams.

Thanks again for opening this discussion- I hope to meet you at a conference sometime in the future!

References
1. Allen, H.K., Moe, L.A., Rodbumrer, J., Gaarder, A., & Handelsman, J., 2009. Functional metagenomics reveals diverse b-lactamases in a remote Alaskan soil. ISME 3, pp. 243-251.
2. Aminov, R.I., 2011. Horizontal gene exchange in environmental microbiota. Front. Microbiol. 2,158 doi:10.3389/fmicb.2011.00158.
3. Corinaldesi, C., Danovaro, R. & Dell‘Anno, A., 2005. Simultaneous recovery of intracellular and extracellular DNA suitable for molecular studies from marine sediments. Appl. Environ. Microbiol. 71, pp. 46-50.
4. D’Costa, V.M., McGrann, K.M., Hughes, D.W., & Wright, G.D., 2006. Sampling the antibiotic resistome. Science 311, pp. 374-377.
5. McKinney, C.W., Loftin, K.A., Meyer, M.T., Davis, J.G., & Pruden, A., 2010. tet and sul antibiotic resistance genes in livestock lagoons of various operation type, configuration, and antibiotic occurrence. Environ. Sci. Technol. 44 (16), pp. 6102-6109.
6. Peak, N., C.W. Knapp; R.K. Yang; M.M. Hanfelt; M.S. Smith, D.S. Aga, & Graham, D. W., 2007. Abundance of six tetracycline resistance genes in wastewater lagoons at cattle feedlots with different antibiotic use strategies. Environ. Microbiol. 9 (1), pp. 143–151.
7. Wu, J. F. & Xi, C. W., 2009. Evaluation of different methods for extracting extracellular DNA from the biofilm matrix. Appl. Environ. Microbiol. 75, pp. 5390-5395.

Why viewing antibiotic resistance genes as a pollutant is a problem

It is not uncommon that scientists, especially researchers active within the environmental field, view antibiotic resistance genes (ARGs) as pollutants (e.g. Pruden et al. 2006). While there are practical benefits of doing so, especially when explaining the threat of antibiotic resistance to politicians and the public, this generalization is a little bit problematic from a scientific view. There are several reasons why this view is not as straightforward as one might think.

The first is that ARGs does not spread the same way as pollutants do. ARGs are carried in bacteria. This means that ARGs cannot readily be transferred into, e.g. the human body by themselves. They need to be carried by a bacterial host (ARGs present on free DNA floating around is of course possible, but likely not a major source of ARG transmission into new systems). Therefore, when we find resistance genes in an environment, that is an extremely strong indication of that we also have resistant bacteria. Also, finding ARGs is not necessarily an indication of high levels of antibiotics, as the resistance genes can remain present in the bacterial genome for extended periods of time after exposure (Andersson & Hughes 2011).

The second reason why ARGs should not be viewed as pollutants is that they are not. If anything, the ARGs contribute to the resilience of the ecosystem towards the actual toxicants, which are the antibiotics themselves. Having a resistance gene is an insurance that you will survive antibiotic perturbations. Calling ARGs pollutants just deflects attention from the real problem to nature’s response to our contaminant.

What we have to do is not to try to defeat the resistance itself, but to try to minimize the spread of it. This means that we need to constantly monitor our usage and possible emissions of antibiotics and try to reduce risk environments as much as possible. Emissions from sewage treatment plants (Karthikeyan & Meyer 2006; Lindberg et al. 2007), hospitals (Lindberg et al. 2004), production facilities (Larsson et al. 2007; Fick et al. 2009) and food production (Davis et al. 2011) are obvious starting points, but we need to continuously monitor sources of antibiotic pollutions. Of course, this is only my view of the problem, but I believe that while the problem for our society lies within the resistance genes, the cause lies within the actual pollutants – the antibiotics we use and abuse.

References

  1. Andersson, D.I. & Hughes, D., 2011. Persistence of antibiotic resistance in bacterial populations. FEMS Microbiology Reviews, 35(5), pp.901–911.
  2. Davis, M.F. et al., 2011. An ecological perspective on U.S. industrial poultry production: the role of anthropogenic ecosystems on the emergence of drug-resistant bacteria from agricultural environments. Current Opinion in Microbiology, 14(3), pp.244–250.
  3. Fick, J. et al., 2009. Contamination of surface, ground, and drinking water from pharmaceutical production. Environmental toxicology and chemistry / SETAC, 28(12), pp.2522–2527.
  4. Karthikeyan, K.G. & Meyer, M.T., 2006. Occurrence of antibiotics in wastewater treatment facilities in Wisconsin, USA. The Science of the total environment, 361(1-3), pp.196–207.
  5. Larsson, D.G.J., de Pedro, C. & Paxeus, N., 2007. Effluent from drug manufactures contains extremely high levels of pharmaceuticals. Journal of hazardous materials, 148(3), pp.751–755.
  6. Lindberg, R. et al., 2004. Determination of antibiotic substances in hospital sewage water using solid phase extraction and liquid chromatography/mass spectrometry and group analogue internal standards. Chemosphere, 57(10), pp.1479–1488.
  7. Lindberg, R.H. et al., 2007. Environmental risk assessment of antibiotics in the Swedish environment with emphasis on sewage treatment plants. Water research, 41(3), pp.613–619.
  8. Pruden, A. et al., 2006. Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environmental Science & Technology, 40(23), pp.7445–7450.

From the literature batch…

A random sample of things from this week’s scientific news I think are worth sharing:

Britain is apparently shutting down many of its climate change outreach efforts. I find this very saddening, and see it as an indication of our extreme short-sightedness. We need to put more effort and funding into preserving the environment – not less. In addition, the economic benefits of taking care of the nature around us will probably be much larger than the small sums we save in the short term by not doing anything. We clearly need better incentives to look beyond the next budget and the next election.

The editorial of Nature Reviews Microbiology points the torch on the need for research within basic microbiology, pointing out that “the functions of many genes in the genomes of even the best studied organisms, such as Escherichia coli and Bacillus subtilis, remain unknown. Often these genes do not resemble other, characterized, genes in the databases, allowing for the possibility that interesting new pathways remain to be discovered. (…) if we want to understand how life works at the molecular level, it is crucial to continue and expand basic microbiology research.” I would like to add that a more complete understanding of at least one model organism would drastically increase the accuracy of genome (and metagenome) annotation in new sequencing projects, which today is patchy, to say the least.