Checking In with the CRISPR Crew

 

CRISPR Crew Header

In the Shariat lab, we are studying Salmonella presence in the Susquehanna River. Although mostly associated with chickens, Salmonella is also found in aquatic environments due to factors like runoff and farming. Earlier this summer we took a three-day sampling adventure up and down the river along with some of our collaborators from the US Food and Drug Administration, to look for Salmonella in both the river itself as well as its tributaries. We split into Team Chicken (North) and Team Cow (South) that sampled six to eight sites per day – all while looking real good in waders (check out the picture of Abby below!). Together, we drove nearly 1000 miles!

 

Abby River

In order to determine the presence of Salmonella in the different sites, the samples were cultured in a variety of media and then plated on nearly 400 plates and left to grow overnight. We used indicator plates to be able to distinguish between Salmonella and other bacterial species found in the river. On the indicator plates we used, Salmonella appears as black colonies. After analyzing all these plates, we used a molecular screening technique to confirm that the colonies were Salmonella. Spoiler alert: we found a whole lot of Salmonella!

Since Salmonella is super diverse, we have been trying to figure out what specific kind of Salmonella was in each sample. In order to do this, we have been analyzing a specific section of bacterial DNA, known as the CRISPR region. From the sequences found in this region, we are able to determine exactly what we are dealing with. In addition to our CRISPR analyses, we are working with the Lamendella Lab at Juniata College to study interactions of microbial communities in the Susquehanna River.

There are two big takeaways from our work so far:

  1. Do not drink the water in the Susquehanna. Ever.
  2. Order your data numerically. Even if you think you can handle it, you can’t. Ordering your data makes it possible to do two weeks of work in just one morning.

Team Chicken and Team Cow hit the road next week for anther sampling trip – round #2, here we come!

Plate Picture CroppedThree plates that we streaked; two are positive for Salmonella (left, center), while the third is negative (right). Both plates came from our favorite site, Beefmaster (we’ve got some stories about this site – you should stop by our lab and ask us!)

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