All of our naturally derived antibiotics come from the ground, or more specifically the organisms that live in the ground. It’s estimated that there are more organisms living in just one square inch of soil than there are humans in the entire world. And we know and understand so very little of what thrives at that level. The bacteria that exist on this plane of existence have been fighting for millions of years, far beyond our own petty rivalries. Their weapons of choice are a variety of antibiotic chemicals, battling to suppress rival bacteria and an almost equal variety of activatable genes that work to rebuff any counter measures. Even in the smallest physical parts of our world, it seems that it really is a jungle out there.

With our widespread overuse of antibiotics, both in humans as well as for our livestock, and the corresponding resistance to the majority of our antibiotics, there is a tremendous push to better understand where the resistance is accurately coming from. Over the last 10 years, a great deal of effort has gone into researching the bacteria resistome where it all began: in the soil. There have been many papers (See Antibiotic Fall from Grace) suggesting that an excess of antibiotics spill out into the ground we live around, which then drive the development of resistant bacteria, which then complete the cycle back into our system. These papers state that we are creating our own worst nightmares and are nearly helpless to prevent it. As further proof of this effect, Gautam Dantas’ lab in Washington University of St. Louis has published several papers finding exact matches between soil bacteria antibiotic-resistant genes which are identical to ones found in clinically resistant bacteria! The findings of one of his lab’s research were published in Science last year. Suddenly, it’s not just a suggestion anymore.

Fiona Walsh seems to have taken a slightly different stand, however. While still focusing on the soil ecosystem and the soil bacterial resistome, she sees a less direct relationship between the clinically resistant genes and the naturally occurring ones in the soil. She began by testing soil samples both from agricultural and urban locations (close to human activity) as well as more pristine locations (with minimal human impact). Walsh was looking to establish the levels of culturable resistant bacteria and identify the different mechanisms of resistance were most often utilized. What she found was over 80% resistance in over 400 isolates to 16-23 of the antibiotic drugs which were screened…even in the pristine locations! There was no relationship at all between the variety of resistance and the level of human activity. Instead, Walsh found a number of bacteria which were able to utilize the efflux capabilities of surrounding resistant bacteria to assume their own resistance. There was also little correlation in her study between the intrinsic resistances of soil bacteria to clinical bacteria. And contrary to Dantas’ findings, Walsh did not find any ESBL (Extended Spectrium β-Lactamases) or quinolone resistant genes in the bacteria she tested (caveat: Walsh primarily tested in Switzerland, while Dantas’ work was across the US).

Ultimately though, everyone agrees that soil bacteria are an important reservoir for resistance mechanisms and that more work needs to be done to understand the myriad mechanisms at play. This research is crucial in our own tiny war against the multitude of bacteria that plague us and academic groups like Dantas’ and Walsh are on the forefront in discovering the rules of this war and using those rules to better treat the diseases caused by those pathogens.

Walsh, F., & Duffy, B. (2013). The Culturable Soil Antibiotic Resistome: A Community of Multi-Drug Resistant Bacteria. PloS one, 8(6), e65567.

Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O., & Dantas, G. (2012). The shared antibiotic resistome of soil bacteria and human pathogens. Science, 337(6098), 1107-1111.

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