Antibiotic-Resistant Bacteria Were Around a Long Time Before Our Antibiotics

But antibiotic overuse isn't off the hook.

Michael Byrne

Michael Byrne

​Image: CDC

​Long before techno-humans had whipped up their first batches of penicillin, antibiotic resistance was already under development within the human gut. This is the implication, anyway, of recently discovered antibiotic resistance genes within the bacterial flora of a South American tribe that, until 2009, had never had contact with the outside world, let alone its antibiotics.

These findings come courtesy of researchers at Washington University St. Louis, led by pathologist Gautam Dantas, and are published in the current issue of Science Advances.

In question is a tribe of Yanomami Amerindians who've gone without outside contact for some 11,000 years, remaining in isolation thanks to a remote region of southern Venezuela known as the High Orinoco, a vast 80,000 square-kilometer tract of jungle marked by bottomless river valleys and soaring mountains. In 2008, the group's village was spotted by a military helicopter and, in 2009, a Venezuelan Ministry of Health mission arrived at the site. To protect the privacy and security of the tribe, the location and name of the village are being kept secret. Only one of the two dozen or so authors behind the current paper actually visited the site.

"These subjects from an uncontacted community therefore represent a unique proxy for the preantibiotic era human resistome," the paper notes. "Here, we characterized the microbiome and resistome of these subjects, and compared them to those of other non-isolated populations. Samples of the oral cavity, forearm skin, and feces were obtained from 34 of the 54 villagers at the time of the first medical expedition." Their ages ranged from four to 50 years.

It wasn't just the presence of antibiotic-resistant bacteria that surprised the researchers—"these Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group," Dantas and his group report.

And, indeed, within that flora are bacteria boasting functional antibiotic resistance (AR) genes—30 in all—of the sort that would be expected had the subjects been exposed to modern synthetic antibiotics. These genes, according to the researchers, are likely poised for mobilization in the event of exposure to pharmacological levels of antibiotics. So, the AR potential of the genes would become actual antibiotic resistance, which is, of course, bad.

Many of the AR genes found among the villagers are targeted at natural antibiotics of the sort produced by soil microbes, but some are advanced enough to potentially offer resistance against semi-synthetic and synthetic antibiotics. "These include, for example, third- and fourth-generation cephalosporins, which are drugs we try to reserve to fight some of the worst infections," Dantas notes. "It was alarming to find genes from the tribespeople that would deactivate these modern, synthetic drugs."

This is likely the result of cross-resistance or the side effect of housekeeping genes, e.g. genes that are required for the maintenance of basic cellular function.

None of this lets the antibiotic abuse and overuse of industrialized humans off the hook. If anything, it shows the precariousness of the whole antibiotic landscape, in which AR genes can be quickly and simply activated by the introduction of powerful pharmacological antibiotics. 

"We've seen resistance emerge in the clinic to every new class of antibiotics," Dantas says in a statement, "and this appears to be because resistance mechanisms are a natural feature of most bacteria and are just waiting to be activated or acquired with exposure to antibiotics."