Skip to comments.Soil May Be Source of Drug-Resistant Bacteria
Posted on 09/01/2012 12:05:04 AM PDT by neverdem
A scoopful of soil, teeming with microscopic life, contains a rich library of genes that help bacteria thrive in the wild. Some of those genes, new research has found, are identical to those that allow disease-causing bacteria in humans to survive antibiotic treatment. The finding suggests that innocuous soil bacteria could be the original source of some antibiotic-resistant genes seen in hospitals.
"Soil ecologists have been predicting for quite a while that the soil acts as a reservoir for resistance," says molecular biologist Jo Handelsman of Yale University, who was not involved in the new study. "But until now there’s been very little evidence."
Soil-dwelling bacteria have been exposed to natural antibiotics—compounds frequently produced by competing microbes—for millions of years, often developing resistance mechanisms as they coevolved. Many of these natural killer compounds have served as the basis for commercially sold antibiotics. Because bacteria are known to swap genes when they come in contact, researchers have speculated that some resistance genes found in the soil may find their way into microbes that cause diseases in humans and animals, such as Escherichia coli or Staphylococcus.
But scanning a soil sample for specific types of genes is tricky because there are so many genes in total, and most bacterial resistance genes found in soil in the past have differed from those seen in human pathogens.
Now, combining next-generation, high-throughput sequencing with classic bacterial culturing methods, biologist Gautam Dantas of Washington University School of Medicine in St. Louis studied 11 soil samples from around the United States. The team first isolated genes from the soil that originated from Proteobacteria, a group of bacteria that’s usually disease-causing, hypothesizing that these organisms might be most likely to share genes with pathogens. Next, they inserted the genes into cells and tested which grew in the presence of any of 12 antibiotics. They then pinpointed 252 genes that survived these antibiotics and further analyzed their gene sequences, comparing them with genes from known human pathogens. One-hundred-ten of the genes had clear similarities in sequence to known antibiotic-resistance genes, the team discovered, and 18 of those were 100% identical to genes found in human pathogens.
The matching sequences likely mean that the genes were transferred at some point between the soil bacteria and the pathogens, the team reports online today in Science. But although it is more likely that they were transferred from the soil to human pathogens, the team can't rule out that it was the other way around. "It's hard to tell is who gave what to whom," Dantas says. "Our work does not speak to the direction of the transfer." Future studies may show how the genes are transferred exactly, he says—and find ways to stop that process.
Further analysis reveals that the antibiotic resistance genes are often lumped together into “resistance islands” within microbes’ DNA, with up to five genes within one island. These clumps of genes are flanked on each end by DNA sequences known as mobility units, which make them prone to moving between genomes as a whole. “In one gene transfer event, you could take a susceptible pathogen and … make it resistant to four or five antibiotics at the same time,” Dantas says.
"I think it's a really sound study with interesting results," Handelsman says. "The high degree of identity they reported is remarkable." One fascinating aspect is that so many resistance-conferring gene sequences didn't show similarity to known resistance genes, she says. Uncovering their mechanisms of resistance could reveal new molecular pathways to target with antibiotics. "Part of the work that’s going to be really interesting in the future is uncovering the functions of some of those genes," she says.
FReepmail me if you want on or off my combined microbiology/immunology ping list.
Ping... (Thanks, neverdem!)
I remember reading of a scientist who scooped soil samples at every airport he arrived at.
Very interesting. Thank you for posting.
WE ARE ALL GONNA DIE!!!!!!!!!!!!!!!!!
I guess that dooms all of us born before the 60’s since most of us played in dirt and went barefoot during hour childhood.
As a matter of fact, I’m 66 and many of my friends and acquaintances have died. I never thought about it but after reading this article in must be the DIRT.
My God! Another “scare story” to frighten the lemmings of America.
BTW...check the picture of the guy digging with red rubber boots on to protect him/her/it for the dangerous dirt.
There is an old country saying that I’ve heard the states: “Unless a kid eats a peck of dirt before he is five, he will be sickly his whole life.” Todays custom of sanitizing everthing in site may kill the weak germs and bacteria but those that are a bit stronger go on the reproduce their resistance and so on until we have some that are resistant to everythig! This is my unscientific observation.
“BTW...check the picture of the guy digging with red rubber boots on to protect him/her/it for the dangerous dirt.”
I need to get a pair of those red boots, not to protect me from the bacteria but from these dang fire ants.
PS: I remember the pediatrician telling me not to keep the kids too clean, a little dirt was good for them.
Oddly enough, the best bet may be to use microorganisms to defeat microorganisms.
For over a hundred years, science has known about “bacteriophages”, microorganisms that consume other microorganisms. It was thought that they could be used to fight pathogens, but by themselves they can’t, because pathogens adapt to them even faster than they do to antibiotics.
But ordinary, “good” bacteria have another way of fighting “bad” bacteria. Simply by “shouldering them out”, physically occupying the living area the pathogens need to function and grow.
Antibiotics, however, change this equation. While used to fight “bad” bacteria, they also damage the “good” bacteria. So if the “bad” bacteria are resistant to that antibiotic, suddenly they have a lot of “wide open space” to live and multiply.
The easiest solution would be to flood the region with good bacteria, so they can again limit the space needed by the bad bacteria.
In the human GI tract, there are about 300-1000 different kinds of bacteria. Of these, only 30-40 varieties of good bacteria take up almost all the space.
One way of boosting their numbers is called “probiotics”, the live bacteria found in yoghurt and some other foods, or even in pill form. A particularly good one is fairly new to the grocery store market, but already available in a few brands. It is called “Kerin”, and is like a yoghurt smoothie. It contains as many as 10 different kinds of good bacteria.
Along with a healthy diet and maintaining good vitamin D levels, such foods are good not just for health maintenance, but recovery from antibiotic-damage to the intestinal flora before the bad bacteria can have a population explosion.
Thanks for the ping!
You’re Welcome, Alamo-Girl!
Taint just Vitamin D, although I am witchoo on that!
Enzymes , Magnesium and keeping oneself alakaline (Drink a shot of Bragg’s Vinegar, put lemon in your water, skip the dang carbs!)
Don’t do flu/HPV/shingles vaccine. Eat healthy and stay away from anti biotics when ever possible.
Ban soil, now!
Regular vinegar is acetic acid. Lemon is acidic. How's that helping to keep alkaline?
Which Enzymes? Recently read an article. Stopped by GNC. DOn’t know which to get?
I can’t remember the science ... it’s been many years of suffering... but the ACV
(apple cider vinegar...Bragg’s is the bomb) and the lemons do the actual opposite to the acid in your system. We are acidic peoples now with our voluminously gross diets, we did not used to be. You can research Paleo diets as an alternative, I only know what worked for me.....I tried everything. Magnesium is missing in all of our diets, sadly. I supplement, it helps me sleep.
I take a pro biotic everyday along with my supplements (C,D,K, MSM, NAC, B complex) I don’t take drugs nor do I take flu shots and live as chemically free as I can.