Thank you to Prof.

Koslicki’s Lab at Penn State for supporting this episode of SciShow. You can click the link in the description  to learn more about their work on metagenomics and computational biology. [♪ INTRO] In the last hundred years, antibiotics  have saved millions of lives and probably helped you  through a few infections, too.

They’re drugs that fight bacteria, so they’re great for treating  a wide variety of illnesses. But misusing antibiotics can speed up  how fast bacteria evolve to resist them. And it has!

Antimicrobial resistance is already related to hundreds of thousands of deaths every year. Understanding how this resistance  happens and what kinds of drug-resistant bacteria are out there is huge  for addressing the problem. But with thousands of kinds of  bacteria on and in everything from people to wastewater, that’s  easier said than done.

So, scientists have turned to a  field called metagenomics for help. And among other places, they’ve learned  that one of the biggest hotspots for antibiotic-resistant bacteria…is hospitals. Like the name implies, metagenomics  is an extension of regular genomics.

Genomics is all about studying an individual  organism’s DNA, including sequencing it, or figuring out what molecules make  up their DNA and in what order. Metagenomics is doing that with the  DNA from a bunch of organisms at once. So, instead of analyzing DNA  from one kind of microbe, metagenomics might involve sequencing  the entire collection of DNA from a community of hundreds of kinds of microbes.

Then, scientists can compare what they  find to a genomic reference database and figure out what kinds of  organisms they’re dealing with and how common they are. This method is especially useful  because you don’t have to separate out every kind of microbe and grow it in  its own dish like with other methods. You can just do a broad survey.

And when it comes to tracking  antibiotic resistance and the numerous kinds of bacteria  involved, metagenomics is huge. For instance, one thing multiple  studies have revealed is that hospitals are a major source of antibiotic-resistant genes, which are basically the genetic material  that allows bacteria to resist these drugs. And one especially notable  hotspot is hospital wastewater.

In a way, that’s not super surprising: Many  hospital patients are given antibiotics. And then, those drugs can end up  in their urine and other waste, which goes down the drain. But the water isn’t just going down the drain.

It’s ultimately ending up in waterways. And if it’s not properly treated,  those antibiotic-resistant genes   are going along with it. If hospitals are going to do something about this, they need to understand what kinds of  bacteria and genes they’re dealing with.

And sequencing the DNA of every  kind of microbe individually probably isn’t realistic. And so: metagenomics! In an August 2021 study  in Frontiers in Microbiology, researchers used metagenomics to  investigate the kinds of bacteria and antibiotic-resistant genes in the  untreated wastewater from three hospitals.

They found 34 antibiotic-resistant  genes among them. They also found that different genes were  more common in some hospitals than others. For instance, the two hospitals that  practiced general medicine had similar kinds of bacteria to each other but were  both different than the third hospital, which focused on oral medicine.

With information like this, hospitals  could do more than just understand the problem: They could change or optimize  how they handle their wastewater. If a hospital or wastewater treatment  plant knows what kinds of bacteria and genes to look out for, they could  customize their treatment system to target those microbes and  stop them from spreading. But it doesn’t end there.

See, it’s not just water that’s  spreading these genes and bacteria: Studies have also found similar  results about hospital air. Like, another paper from 2021 published  in the Chemical Engineering Journal used metagenomics and found  that antibiotic-resistant genes were easily spread in a  commonly-used hallway in a hospital. The study also identified specific  categories of bacteria that hospitals could focus on managing.

Now, the hard thing about antibiotic resistance  is that it’s not just limited to these hotspots. Antibiotic-resistant genes are found everywhere: in the soil, in waterways, and even in our guts. For instance, a 2016 study used metagenomics  to study antibiotic-resistant genes in stool samples from seven hospital  patients, plus a healthy volunteer.

They identified 46 antibiotic-resistant genes. But the catch was that the  genes didn’t match the drugs the patients were being treated with. So, it’s not like the patients  were being given antibiotics, and their gut bacteria were adapting.

Instead, they seemed to have picked up these genes from the general hospital  environment and the larger community. And that’s why keeping tabs on  these microbes is so important. Drug-resistant genes and bacteria are all  over the place, and the better scientists can understand where they come  from and how they’re spreading, the better equipped they’ll  be to do something about it.

So, using antibiotics responsibly and  figuring out how to slow the spread of resistant genes is going to be a team effort. But it’ll also be one that has  a huge impact on a lot of lives. Thanks for watching this episode of SciShow!

And thanks again to the Koslicki Lab at  Penn State for supporting this episode. Their lab focuses on computational biology,  including the analysis of metagenomic data. If you enjoyed this video and would  like to learn more about how biology, computer science, and mathematics  can be used to learn about the world around us, you can check out some of  their papers using the link below. [♪ OUTRO]