Super-bacteria eat antibiotics for breakfast

Blogging on Peer-Reviewed ResearchAntibiotics are meant to kill bacteria, so it might be disheartening to learn that some bacteria can literally eat antibiotics for breakfast. In fact, some species can thrive quite happily on nothing but antibiotics, even at high concentrations.

i-bf95bf8f06bd23298722b5f0b97fd2f0-Bacteria.jpgThe rise of drug-resistant bacteria poses a significant threat to public health and many dangerous bugs seem to be developing resistance at an alarming rate. The headline-grabbing MRSA may be getting piggybacks from livestock to humans, while several strains of tuberculosis are virtually untreatable by standard drugs.

But a startling new study reveals just how widespread antibiotic resistance really is. Gautam Dantas from Harvard Medical School managed to culture antibiotic-eating bacteria from every one of 11 soil samples, taken from farmland and urban areas across the US. All eleven were positively loaded with a diverse group of bacteria that were extremely resistant to a wide range of antibiotics at high concentrations.

Soil super-bugs

In their natural environment, these soil bacteria are frequently exposed to a massive array of antibiotics from plants and other microbes, and have evolved ways of detecting and evading them. These resistant strains act as a living reservoir of innovative genetic means of resisting antibiotics, known as the 'antibiotic resistome'.

Dantas searched for resistant bacteria by culturing colonies that could grow in solutions where antibiotics were their only source of carbon. He tested 18 different antibiotics that are used to kill a variety of different bacterial species. Some of these were natural, others man-made; some were old, others new. But every single one managed to support at least one strain of bacteria. Six of them, including commonly used drugs like penicillin, vancomycin, ciprofloxacin and carbenicillin, even managed to feed bacteria from all 11 soils.

The degree of resistance in the soil bacteria was nothing short of extraordinary. Dantas cultured a representative set of 75 resistant strains and found that on average, they resisted 17 of the 18 antibiotics at low concentrations of 20 milligrams per litre (full bars in image below). But even at higher concentrations of 1 gram per litre (filled bars in image below), each strain managed to stand firm against an average of 14 out of 18 drugs.


When Dantas studied some of these strains more closely, he found that they nullified the drugs using similar techniques to the drug-resistant versions of disease-causing bacteria. Some shunted the antibiotics out of their cells with molecular pumps, others used enzymes to cut up the drugs, and yet others reprogrammed their own genetic code to deprive antibiotics of their targets.

Reservoir of resistance

The real danger is that the soil-living species could provide new defences that more dangerous ones can draw on to shrug off our best drugs.  Bacteria are capable of passing genetic material between one another as easily as two humans might swap business cards, making it trivial for the soil super-bugs to pass their crucial genes on to more dangerous species. To see how easily this could happen, have a look at this earlier post about how the food poisoning bug Salmonella has passed a resistance gene on to the Black Death bacterium. 

In principle, bacteria should be more able to successfully take up resistance genes from other closely related species. It's worrying then that Dantas's antibiotic-eaters belonged to such diverse groups.  By establishing a family tree of the different strains, he found that they were members of at least 11 different bacterial groups, although over half of them came from just two orders - the Burkholderiales and the Pseudomonadales. These include a wide variety of species that are known to infect hospital patients with weakened immune systems.

They are known for their large genome sizes (well, large for bacteria anyway) and some groups have suggested that these sizeable genomes allow them to metabolise a wide range of chemicals, antibiotics included. This unusual diet will come as no surprise to many a microbiologist. Bacteria can colonise some of the most extreme environments on the planet and can survive on the most unlikely to food sources, from crude oil to toxic waste. Now, it seems that they can also survive solely on chemicals that are meant to kill them.

Images from Science

Reference: doi:10.1126/science.1155157

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forgive my ignorance, but do we know if this is a new phenomenon? In other words, what if this study had been done 20, 50, 100 yrs ago? Would we expect that no bacteria would thrive off any of the antibiotics? In other, other words, is modern antibiotic use driving the evolution of these soil bacteria or is this an example of profound genetic variation in soil bacteria?

My guess is that it's not new. A lot of antibiotics are natural ones (think penicillin) and soil bacteria would presumably be exposed to them naturally. But I don't think it's clear - the authors suggest that these bacteria could act as a reservoir for resistance traits in disease-causing species, but I wonder if it could also work the other way round. Anyone else want to chip in?

My understanding is that its not a new phenomenon, but their abundance is relatively new. Previously having antibiotic resistance would have been very handy on occasion, but only in particular environments. However these days we have pumped the environment so full of antibiotics (mostly for agricultural purposes) that even areas that you would consider to be fairly pristine (such as Antarctica) are now returning positive to antibiotic resistant bacteria.

The thing to keep in mind is that its such a massive selective pressure. Most genetic advantages are fairly minimal. Using extra food sources, or using them more efficiently means that you should manage to be able to fuel your reproduction more frequently meaning there are a few more of you around. With antibiotics its either you have the resistance or you are dead (more or less) so the advantage to a particular individual is huge.

Thanks for the link to the article on antibiotic-resistant MRSA. Antibiotics are commonly given to feeder stock animals in the feed of the animal for the primary purpose of growth promotion. It would appear that that use of antibiotics in the feed, when there is no other sign of disease would not be warranted in the light of this new information. Of course without some regulation and enforcement, that leaves us with a moral argument to operators who feed antibiotics to animals for the primary purpose of increased growth to begin with.

To answer Jim, Ed, there have been antibiotics in the soil for millennia especially as produced by Streptomyces species. In fact, more than half of our currently used antibiotics are natural products derived from bacteria and fungi (or are semi-synthetic analogs thereof). The mechanisms described in this exciting paper have largely evolved as biological defense mechanisms over time that predates us - while we can find antibiotics in the water and soil from our current use, the concentrations pale in comparison with the local concentrations produced by soil bacteria and fungi.

does it affect animals

By brandon guerrero (not verified) on 13 Jan 2009 #permalink