Menus Subscribe Search
bacteria

(PHOTO: MICHAEL DESIGN/SHUTTERSTOCK)

Living in a Bacterial World

• September 16, 2013 • 10:00 AM

(PHOTO: MICHAEL DESIGN/SHUTTERSTOCK)

The good news: Antibiotics didn’t create antibiotic-resistant bacteria. The bad news: Antibiotic-resistant bacteria is everywhere.

The discovery of antibiotics was one of the greatest medical breakthroughs in human history, but it was quickly followed by the rise of antibiotic-resistant pathogens. Now, nearly 80 years after the introduction of antibiotic drugs, multi-drug-resistant bacteria plague hospitals, and once-tamed diseases like tuberculosis are making a comeback. But where exactly do human pathogens acquire the genes that make them resistant to antibiotics? New research shows that the answer could be … everywhere.

The widespread problem of antibiotic-resistant pathogens is commonly blamed on the fact that we use antibiotics too aggressively: physicians overprescribe them and farmers routinely keep their livestock on them. This is a problem because, as the story goes, by saturating ourselves and our environment with antibiotics we’ve created conditions ripe for the evolution of antibiotic-resistant bacteria. Since bacterial populations tend to range in the trillions, it’s not surprising that there will be a few individuals bearing a lucky mutation that enables them to survive and reproduce in the presence of antibiotics. To avoid this evolutionary scenario, we need to limit our use of antibiotics to situations when they are absolutely necessary.

We’re swimming in a vast reservoir of antibiotic resistance genes.

As it turns out, this evolutionary story is too simple. Bacteria have a fast track to antibiotic resistance because they have the ability to swap genes. Bacteria are generous with their genes, sharing them even with members of other bacterial species. The possibility of bacteria trading antibiotic resistance genes was first suggested in the 1950s, and in a groundbreaking paper in 1973, two scientists showed that common soil bacteria and pathogenic Streptomyces share the same specific type of resistance to the drug gentamicin. However, for decades there was not much evidence that gene swapping with environmental bacteria played a major role in the emergence of resistant pathogens.

That evidence is now coming in, and it shows that we’re swimming in a vast reservoir of antibiotic resistance genes. Using a new method called “functional metagenomics,” scientists are searching for resistance genes by collecting bacterial DNA from the environment and testing its function in harmless lab bacteria. Researchers have collected DNA from a wide range of environments, including the human gut, city soil, remote Alaskan wilderness, processed sewage, and even 30,000 year old Beringian permafrost. Antibiotic resistance genes were found in each of these environments.

Human pathogens are swapping resistance genes with these environmental reservoirs. Last year, my Washington University colleagues working in the laboratory of Gautam Dantas reported that they had found seven resistance genes in soil bacteria that were completely identical to genes in pathogens from human clinical samples. This finding is the strongest evidence to date that pathogenic bacteria are exchanging resistance genes with bacteria in the environment. As scientists scour the newly accessible genetic landscape of our bacterial environment, they will uncover many more examples.

Perhaps more disturbing than the swapping of antibiotic resistance genes is what has not yet been shared. Dantas and other scientists have discovered dozens of exotic new types of antibiotic resistance genes that have not yet been seen in human disease, but which are out there lying in wait. Many of these genes appear to have normal functions that do not involve defeating antibiotics, but they can be recruited for antibiotic resistance when the host bacteria is exposed to a drug. Because these genes have functions unrelated to antibiotics, they can hang around in the bacterial population even without the evolutionary pressure of antibiotic overuse.

These recent studies show that genetic reservoirs of antibiotic resistance are everywhere, and that the capacity to defeat antibiotics existed long before humans began using antibiotic drugs. While there is no question that our overly aggressive use of antibiotics has contributed to the rapid spread of drug-resistant pathogens, resistance was going to show up sooner or later regardless of how judiciously we used antibiotics. Cutting down on our antibiotic use at this point is important, but it is a delaying action; we need a new strategy. In a recent review of the new functional metagenomic studies, Dantas and his colleagues point to a few possibilities: antibacterial vaccines, and viruses that prey on bacteria. Strategies like these are largely in their infancy, but they will be crucial in our ongoing battle with pathogens.

Michael White
Michael White is a systems biologist at the Department of Genetics and the Center for Genome Sciences and Systems Biology at the Washington University School of Medicine in St. Louis, where he studies how DNA encodes information for gene regulation. He co-founded the online science pub The Finch and Pea. Follow him on Twitter @genologos.

More From Michael White

A weekly roundup of the best of Pacific Standard and PSmag.com, delivered straight to your inbox.

Recent Posts

September 12 • 4:00 PM

Life, Liberty, and the Pursuit of Plastic Bags

California wants you to pay for your plastic bags. (FYI: That’s not an infringement on your constitutional rights.)


September 12 • 2:00 PM

Should We Trust the Hearts of White People?

On the 50th anniversary of the Civil Rights Act, revisiting a clip of James Baldwin on the Dick Cavett Show.


September 12 • 12:00 PM

Big Government, Happy Citizens?

You may like to talk about how much happier you’d be if the government didn’t interfere with your life, but that’s not what the research shows.


September 12 • 10:00 AM

Whispering in the Town Square: Can Twitter Provide an Escape From All Its Noise?

Twitter has created its own buzzing, digital agora, but when users want to speak amongst themselves, they tend to leave for another platform. It’s a social network that helps you find people to talk to—but barely lets you do any talking.


September 12 • 9:03 AM

How Ancient DNA Is Rewriting Human History

We thought we knew how we’d been shaped by evolution. We were wrong.


September 12 • 8:02 AM

Give Yourself a Present for the Future

Psychologists discover that we underestimate the value of looking back.


September 12 • 8:00 AM

I Walked Through the Financial Crisis

Why are former Wall Street employees guiding tourists around the Financial District? Paul Hiebert signed himself up and tried to find out.


September 12 • 7:05 AM

Scams, Scams, Everywhere


September 12 • 6:17 AM

In Soccer as in Art, Motifs Matter

A new study suggests a way to quantitatively measure a team’s style through its pass flow. It may become another metric used to evaluate potential recruits.


September 12 • 4:00 AM

Comfort Food Is a Myth

New research finds that, contrary to our beliefs, such foods don’t have any special ability to improve our moods.



September 11 • 4:00 PM

Reading the Camouflage Uniforms in Ferguson: ‘You Are Now Enemy Combatants’

Why are police officers wearing green or desert camouflage in a suburban environment?


September 11 • 2:00 PM

Wage Theft: How Two States Are Fighting Against Companies That Categorize Employees as Independent Contractors

New York and Illinois have passed hard-nosed laws and taken an aggressive tack toward misclassification.


September 11 • 11:03 AM

Yes, I’m a Good Person. But Did You Hear About Her?

A new study tracks how people experience moral issues in everyday life.


September 11 • 11:00 AM

Searching for Everyday Morality

Experimenters use text messages to study morality beyond the lab.


September 11 • 8:00 AM

The Geography of Uber

If it continues to grow—and there are few reasons to think it won’t—will Uber transform the infrastructure of cities or glom onto what’s already there?



September 11 • 6:05 AM

One Man’s Search for an Orgasmic Life Force

It remains unclear what “orgone” actually is, but Wilhelm Reich thought you could find it by sitting inside a box.


September 11 • 4:03 AM

Jack the Ripper’s DNA: Was Aaron Kosminski Behind the Whitechapel Murders?

Russell Edwards says he’s solved the mystery. His proof might be a little threadbare.



September 10 • 4:00 PM

The Average White American’s Social Network Is Just One Percent Black

And three-quarters of white Americans report that they haven’t had a meaningful conversation with a single non-white person in the last six months.


September 10 • 2:00 PM

Eye on the Fly

The tiny fruit fly has been beloved by developmental biologists for more than a century. Turing patterns may yet explain its shape.


September 10 • 10:02 AM

Why Do Women Earn Less as Mothers and Men Earn More as Fathers?

For women, becoming a parent means you can expect to earn even less over your lifetime—unless you’re Marissa Mayer.



September 10 • 7:00 AM

Is Back Pain Ruining Your Sex Life?

You might be doing it wrong.


Follow us


Big Government, Happy Citizens?

You may like to talk about how much happier you'd be if the government didn't interfere with your life, but that's not what the research shows.

Give Yourself a Present for the Future

Psychologists discover that we underestimate the value of looking back.

In Soccer as in Art, Motifs Matter

A new study suggests a way to quantitatively measure a team’s style through its pass flow. It may become another metric used to evaluate potential recruits.

Searching for Everyday Morality

Experimenters use text messages to study morality beyond the lab.

Is Back Pain Ruining Your Sex Life?

You might be doing it wrong.

The Big One

One country—Turkey—produces more than 70 percent of the world's hazelnuts. September/October 2014 new-big-one-2

Copyright © 2014 by Pacific Standard and The Miller-McCune Center for Research, Media, and Public Policy. All Rights Reserved.