Notes from the Lab: Genome Sequencing for Dummies

Genome sequencing is when we break open cells, make them spill their DNA into small test tubes, then we use fluorescent dyes, high-power cameras and a special mix of enzymes to read the order of the Gs, As, Ts and Cs that make up each organism’s genetic code. You can do this for any organism, big or small. But, here at ARAC, we do it mostly for bacteria. Knowing the order of the letters -- called nucleotides or bases -- helps us figure out where the bacteria have come from, how likely they are to cause disease, and how resistant they are to antibiotics. Kind of like how a family tree tells us our ancestry or how likely we are to have blue eyes or develop a certain disease. Genome sequencing gives us even more detail to track important trends with particular bacteria of interest. Using this information, we hope to figure out new ways to stop superbugs from spreading and causing disease.

Genome science has a rich history, going as far back as 1871 when Friedrich Miescher published a paper identifying the presence of ‘nuclein’, now known as DNA, in the cell nucleus. It was not until 1995 when the first bacterial genome sequencing was completed, a watershed moment in microbiology. Thanks to this technology, we are able to recognize patterns of disease that were impossible to see in the past. >Here at ARAC, we use genome sequencing in most of our research, including our recent Foodborne Urinary Tract Infection (FUTI) study. This study looked at whether the bacteria that commonly causes UTIs is the same bacteria that can be found in retail meat. We tested thousands of meat and poultry samples from large grocery stores, collected samples from individuals suffering from UTIs at a local hospital, performed genome sequencing on all of them, and then compared the code to see how related all the samples were. Turns out, they were pretty similar, and in some cases they were almost indistinguishable. These findings suggest that the people suffering from UTIs contracted the pathogen from meat they consumed or handled.

With information like this, we can advise policy makers to focus efforts on strategies to reduce the amount of bacteria on meat and poultry, increase monitoring of bacteria in the food supply, cut antibiotic use in livestock to slow the development of resistant bacteria that spread to people, and minimizing the transfer of these bacteria during food processing and preparation. Thanks to genome sequencing, we hope to identify and better understand the origins of antibiotic-resistant bacteria and prevent them from spreading in our hospitals and communities.