Visualizing the evolution of bacterial resistance

You have probably already seen this. It’s pretty amazing and beautiful and I watched it more than once (although I won’t say how many times….). If by some chance you didn’t catch this fantastic video, don’t fret, I’m here to make sure you don’t miss it.

Baym et al., 2016. Supplemental Figure 3A.

A hot topic lately, specifically related to microbial evolution, is studying the development of antibiotic resistance in strains of bacteria that are involved in human related diseases. Because, as we know, we are totally surrounded by / colonized by / helped (and sometimes) hurt by the microbial world that we live in.

Understanding the development of resistance is tricky, and linked to studying bacterial competition. Although it’s impossible to see the microbes around us with the naked eye, they are in a world filled with their own friends and enemies, (for a nice review, check this out) teasing apart their relationships with each other and fitting that into a global picture of how the world works is no small task.

The Kishony lab at Harvard earlier this month figured out how to VERY eloquently visualize the evolution of this resistance over an incredibly short period of time (less than 2 weeks!), the video is seriously beautiful. Here is a good page to check it out and get a really brief summary of the overall study. Basically, they made a giant petri dish they named the “microbial evolution and growth arena (MEGA)” plate (60 cm wide, 120 cm long)  to clearly visualize mutation and selection in a bacterial population. MEGA is shaped as a, lets say American football field, since the season is upon us.

Baym et al, 2016. Figure 1. The game plan: imagine in the agar between the 0 and 10 yard lines on both sides of the field there is media to keep bacteria happy with no antibiotic, between the 10 and 20 there is a relatively low concentration of antibiotic, then the 20 to 30 a slightly higher concentration etc, with the highest concentration right down the middle of the plate. A thin layer of soft agar that E. coli can move through is laid over the “field”, called the “swim agar”. As you see in the movie, the E. coli start in the area without antibiotic, soon deplete the nutrients and move (by chemotaxis) to other areas on the plate. The antibiotics tested were trimethoprim (often used to treat bladder infections) and ciprofloxacin (used for a wide variety of infections and is also known as “cipro”).

The results are amazing, you can see that at each point where the concentration in antibiotic changes, there is a lag and then growth at distinct points begins, where something has happened that allowed the colonization of the higher concentration of antibiotic to happen. One of the most interesting results from this study was the need for the bacteria to be exposed to intermediate concentrations of antibiotic in order to evolve, the authors found that bacteria were unable to adapt directly from zero to the highest concentration of either drug.Baym et al., 2016. Figure 2

As you might imagine, the fun is just getting started, Baym and colleagues then looked at what nucleotide level mutations had occurred in the strains that allowed them to evolve into a so-called “superbug”. A total of 231 isolates from the MEGA plate with multiple concentrations of antibiotic were sequenced using the Illumina HiSeq platform, while 20 isolates that were grown on MEGA with fewer intermediate steps were sequenced using Illumina MiSeq. If you look through the study, there is an interesting suite of different experiments they tried using essentially different configurations of antibiotic concentrations with MEGA.

Baym et al., 2016. Figure 3. The authors characterized the sequenced isolates as either “minimally” or “highly” mutated and found that the “highly” mutated isolates all had mutations in dnaQ (aka mutD) that encodes DNA polymerase II (essential in proofreading, so yeah, that makes sense). Overall, they found that the “highly” mutated strains had a close to neutral ratio of non-synonymous to synonymous substitutions, while the less mutated strains had a high bias toward coding mutations, suggesting that these guys mainly had adaptive mutations. Also, interestingly, mutations leading to higher resistance usually led to strains with decreased growth rates, demonstrating that there’s generally a cost associated with being able to deal with higher concentrations of antibiotics.

The authors suggest a bunch of other reasons that MEGA might be helpful in a laboratory setting. For example, other organisms can be grown on such a set up, and other ‘challenges’ can be tested, such as different nutrient concentrations or media types, in order to visualize evolutionary dynamics when organisms are exposed to different selection pressures. A picture is supposedly worth a thousand words, and I’m not sure about the math in translating how many  words this movie is worth, but for everyone ranging from researchers at a lab bench, to basically anyone interested in the world around them, this study is pretty cool and the visualization revolutionary.

References

Baym, M., Lieberman, T.D., Kelsic, E.D., Chait, R., Gross, R., Yelin, I. and Kishony, R., 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science, 353(6304), pp.1147-1151.

Ghoul, M. and Mitri, S., 2016. The Ecology and Evolution of Microbial Competition. Trends in Microbiology.

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About Kelle Freel

I'm currently a postdoc working at the Hawai'i Institute of Marine Biology with Dr. Mike Rappé. I'm interested in the biogeography and ecology of microbes, especially of the marine variety. After studying a unique genus of marine bacteria at Scripps Oceanography in grad school, I moved to France, where I worked with a group studying yeast population genomics. In my free time, I like to do outdoorsy stuff, travel, and cook.
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