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Bacteria isolated for four million years beat newest antibiotic

Ancient bacteria share genes with bugs exposed to modern medicine

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Bacteria found deep inside a cave that has had scant exposure to the outside world for at least four million years share some of the same antibiotic-resisting traits that other bugs are supposed to have developed in response to modern medicines.

That’s the finding of a new research article, Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome, which plumbed the depths of Lechuguilla Cave, a 200-kilometre long cave in New Mexico, USA, to find bacteria populations that have had little or no exposure to the outside world.

“The deep recesses of Lechuguilla Cave,” the article says, were “isolated from surface input for the past 4–7 million years, [and] therefore provide a unique environment to study the presence and prevalence of antibiotic resistance elements.” The areas of the cave chosen for collection of bacteria samples have been visited by humans, but only by 4-6 people, and the paper says “The cave’s geologic features, including the impermeable siltstone caprock which prevents rapid influx of surface water, great depth, and long isolation from the surface, rules out the possibility of exposure to anthropogenic use of antibiotics as well as antibiotic contamination through water bodies.”

An expedition to the caves harvested 93 different bacteria, many of which displayed resistance to antibiotics. Some were even resistant to daptomycin, a substance the article says is “the newest class of antibiotic approved for clinical use.”

“Like surface organisms, the majority of these strains were multidrug resistant indicating that antibiotic resistance is a common and widespread phenotype in pristine, unimpacted environments,” the paper says, but also notes “differences in the pattern of resistance” were evident between the cave-dwellers and bacteria that have been exposed to Register readers.

The article goes on to suggest that “The presence of multidrug resistant organisms even in this pristine environment reinforces the notion that the antibiotic resistome is an ancient and pervasive component of the microbial pangenome.” Further analysis showed that bacteria from the cave share genes with surface bacteria known to have developed antibiotic resistant traits.

In other words, bacteria are already good at battling antibiotics, so it’s not entirely safe to assume anthropogenic antibiotics have created an evolutionary hothouse that forces bacteria to defend themselves.

But the study also admits it has worked with a very small sample and says the bugs it found “… very likely have not been evolved simply to evade the effects of molecules that we have termed antibiotics.”

“This fact further underlines the importance of the judicious use of antibiotics to avoid selection of existing resistance elements and their subsequent mobilization through microbial communities thereby limiting the effectiveness of these drugs to treat infectious diseases,” the paper says. ®

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