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Blogging from the NW ASM branch meeting, part II

Yesterday, I wrote about the some of present (and future) methods that are (or will be) used in clinical labs to identify pathogenic microbes. In these next two posts, I want to describe the talks I attended on antibiotic resistance, from Xuan Qin and Fred Tenover (CDC), and some new things that I learned.

How do bacteria survive when their human hosts take a lot of antibiotics?

Children’s Hospital (Seattle) routinely sees about 200 children with cystic fibrosis. Cystic fibrosis is a genetic disease that only appears when you have two copies of a CFTR gene with mutations. Normally, the protein that the CFTR gene encodes works to transport chloride ions across the cell membrane. When a mutant form of this protein is produced, it doesn’t function very well and for reasons that I don’t entirely understand, the lungs fill up with a gooey mucus that leaves CF patients susceptible to bacterial diseases and all sorts of rotten health problems.

To fight off all these bacterial infections, CF patients take antibiotics more often and more frequently than most people. In fact, the impression I got from the talk is that these kids are on antibiotics all the time.

What antibiotics are around, bacteria do whatever takes

i-f52bcf533b815a2371c6df1114977de8-211393452_3983735d43.jpgDr. Qin found that bacteria start acting weird. In fact, you can isolate pure cultures from several different kinds of bacteria that grow in the lungs of kids with CF, and streak them out, and see the colony phenotypes practically change before your eyes.

[This image comes from jpshlumbohm's photostream.
I picked it to show what colonies can look like on a plate.]

A pure culture, by definition, is a culture where all the bacteria were derived from a single cell. Most of the time, if you dilute these bacteria in broth and spread them out on a plate so that each new colony is started from a single cell, all the colonies will look alike. They’ll be similar to each other in size, shape, texture, and color. But, if you isolate pure cultures of bacteria from CF patients, and plate them, you see that the bacteria are, in fact, different sizes, even though they came from a single cell. Some are normal sized and some are small. Dr. Qin called the small colony variety, “Small colony variants.”

This morphing act isn’t limited to one type of bacteria either. She found it happening with Pseudomonas, Klebisiella, Stenotrophomonas maltophilia, and probably some others that I missed writing down.

What are these strange small colony variants?

They are antibiotic resistant, that’s for sure.

How do they avoid being killed?
These bacteria seem to use a mechanism that I wrote about before: “persistence is resistance.

Not only do these bacteria make small colonies on a plate, they grow slowly in broth relative to the others, and they even make smaller cells.


Or as Dr. Qin put it, what do these bacteria do to make themselves sick? Do we just have a case of anorexic bacteria?

One thing that we know is that they’ve developed some new dependencies. Where before they could look at heme (figuratively, I know they don’t have eyes) and take it or leave it, now they can’t live without it. They need methionine and thymidine, too, where before they could make their own.

The 64 million question then is this: is this genetic change reversible?

Maybe. If this is a reversible phenotype, there are some interesting bioinformatics experiments to do once the genome sequence is in hand. Other bacteria can turn genes on or off by flipping the sequences around. It’s possible that these bacteria are controlling their own growth rates by doing a similar thing.

I’m looking forward to learning the answer.


  1. #1 Mike the Mad Biologist
    March 13, 2007

    I was under the impression (possibly quite false) that some of the small colony variants from CF patients were associated with genome reductions. Was that mentioned?

  2. #2 Sandra Porter
    March 13, 2007

    I was wondering about, too, but Dr. Qin seemed to think that they’d been able to revert to prototrophy when they grew them for awhile in the lab. If you could recover from being an auxotroph, it would imply that the genes are still there, at least in some form.

    She was kind of hesistant on that point, though and when I asked if they’d looked at the genome yet, she said that it (S. maltophilia) is just getting now getting sequenced at the Sanger center.

    It could be also that different species of bacteria use different mechanisms to adapt to these conditions and form small colony variants. One strain might delete some genes, another might invert them, in another, some of the genes might be on a phage that excises from the genome when the going gets rough.

  3. #3 Jaison Jacob
    May 29, 2008

    I have read that scvs can be isolated from virtually all bacterial species (review article by Dr. Richard Proctor, Nature Microbiology Reviews). If that is the case, why scvs are important only in CF,osteomyelitis etc.?(In many of the articles on scvs, researchers isolate them from these two conditions). Apart from disease conditions,what is their role normally?

  4. #4 Sandra Porter
    May 29, 2008


    What is the normal role of small colony variants? I think that’s a great question. I don’t know the answer, but I’m happy to speculate (i.e. – make something up)

    I suspect that colonies are smaller because the bacteria grow slower. Slow growth could be an advantage since it would allow bacteria to persist for a longer time under adverse conditions. In other words, they hang around and grow slow until there’s more food and better times.